NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|297307123|ref|NP_001171992|]
View 

zinc finger protein 75D isoform 2 [Homo sapiens]

Protein Classification

KRAB domain-containing zinc finger protein( domain architecture ID 12029772)

KRAB (Kruppel-associated box) domain-containing zinc finger protein (KRAB-ZFP) plays important roles in cell differentiation and organ development and in regulating viral replication and transcription; KRAB (Kruppel-associated box) domain-containing zinc finger protein (KRAB-ZFP) plays important roles in cell differentiation and organ development, and in regulating viral replication and transcription

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
SCAN pfam02023
SCAN domain; The SCAN domain (named after SRE-ZBP, CTfin51, AW-1 and Number 18 cDNA) is found ...
 45-133 1.61e-47

SCAN domain; The SCAN domain (named after SRE-ZBP, CTfin51, AW-1 and Number 18 cDNA) is found in several pfam00096 proteins. The domain has been shown to be able to mediate homo- and hetero-oligomerization.


:

Pssm-ID: 460417 [Multi-domain]  Cd Length: 89  Bit Score: 157.26  E-value: 1.61e-47
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297307123   45 PESACRHFWSFRYHEATGPLETISQLQKLCHQWLRPEIHSKEQILEMLVLEQFLSILPKETQNWVQKHHPQNVKQALVLV 124
Cdd:pfam02023   1 PEASRQRFRQFCYQEAEGPREALSQLRELCHQWLRPEKHTKEQILELLVLEQFLTILPEEIQSWVREHHPESGEEAVALA 80


                  ....*....
gi 297307123  125 EFLQREPDG 133
Cdd:pfam02023  81 EDLLLERGE 89
KRAB pfam01352
KRAB box; The KRAB domain (or Kruppel-associated box) is present in about a third of zinc ...
 139-180 2.34e-18

KRAB box; The KRAB domain (or Kruppel-associated box) is present in about a third of zinc finger proteins containing C2H2 fingers. The KRAB domain is found to be involved in protein-protein interactions. The KRAB domain is generally encoded by two exons. The regions coded by the two exons are known as KRAB-A and KRAB-B. The A box plays an important role in repression by binding to corepressors, while the B box is thought to enhance this repression brought about by the A box. KRAB-containing proteins are thought to have critical functions in cell proliferation and differentiation, apoptosis and neoplastic transformation.


:

Pssm-ID: 460171  Cd Length: 42  Bit Score: 77.90  E-value: 2.34e-18
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 297307123  139 LLTFEDVAVYFSEEEWQLLNPLEKTLYNDVMQDIYETVISLG 180
Cdd:pfam01352   1 SVTFEDVAVDFTQEEWALLDPAQRNLYRDVMLENYRNLVSLG 42
COG5048 COG5048
FOG: Zn-finger [General function prediction only];
283-397 1.80e-05

FOG: Zn-finger [General function prediction only];


:

Pssm-ID: 227381 [Multi-domain]  Cd Length: 467  Bit Score: 46.61  E-value: 1.80e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297307123 283 SDLIKHHRIHTGEKPYKCQQCDRRFRWSSDLNKHFMTHQGI-KPYRCSWCGKSFSHNTNLHTHQR--IHTGE--KPFKCD 357
Cdd:COG5048  246 SSLSSSDSSSSASESPRSSLPTASSQSSSPNESDSSSEKGFsLPIKSKQCNISFSRSSPLTRHLRsvNHSGEslKPFSCP 325

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|..
gi 297307123 358 E--CGKRFIQNSHLIKHQRTHTGEQPYTCSLCKRNFSRRSSL 397
Cdd:COG5048  326 YslCGKLFSRNDALKRHILLHTSISPAKEKLLNSSSKFSPLL 367
zf-C2H2 pfam00096
Zinc finger, C2H2 type; The C2H2 zinc finger is the classical zinc finger domain. The two ...
 270-292 7.45e-04

Zinc finger, C2H2 type; The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger. #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C] Where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter.


:

Pssm-ID: 395048 [Multi-domain]  Cd Length: 23  Bit Score: 36.51  E-value: 7.45e-04
                          10        20
                  ....*....|....*....|...
gi 297307123  270 FKCQECGKSFRVSSDLIKHHRIH 292
Cdd:pfam00096   1 YKCPDCGKSFSRKSNLKRHLRTH 23
 
Name Accession Description Interval E-value
SCAN pfam02023
SCAN domain; The SCAN domain (named after SRE-ZBP, CTfin51, AW-1 and Number 18 cDNA) is found ...
 45-133 1.61e-47

SCAN domain; The SCAN domain (named after SRE-ZBP, CTfin51, AW-1 and Number 18 cDNA) is found in several pfam00096 proteins. The domain has been shown to be able to mediate homo- and hetero-oligomerization.


Pssm-ID: 460417 [Multi-domain]  Cd Length: 89  Bit Score: 157.26  E-value: 1.61e-47
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297307123   45 PESACRHFWSFRYHEATGPLETISQLQKLCHQWLRPEIHSKEQILEMLVLEQFLSILPKETQNWVQKHHPQNVKQALVLV 124
Cdd:pfam02023   1 PEASRQRFRQFCYQEAEGPREALSQLRELCHQWLRPEKHTKEQILELLVLEQFLTILPEEIQSWVREHHPESGEEAVALA 80


                  ....*....
gi 297307123  125 EFLQREPDG 133
Cdd:pfam02023  81 EDLLLERGE 89
SCAN smart00431
leucine rich region;
45-155 1.76e-44

leucine rich region;


Pssm-ID: 128708 [Multi-domain]  Cd Length: 113  Bit Score: 150.15  E-value: 1.76e-44
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297307123    45 PESACRHFWSFRYHEATGPLETISQLQKLCHQWLRPEIHSKEQILEMLVLEQFLSILPKETQNWVQKHHPQNVKQALVLV 124
Cdd:smart00431   1 PEIFRQRFRQFRYQETSGPREALSRLRELCRQWLRPELHTKEQILELLVLEQFLTILPGELQAWVREHHPESGEEAVTLL 80

                           90       100       110
                   ....*....|....*....|....*....|.
gi 297307123   125 EFLQREPDGTKNESLLTFEDVAVYFSEEEWQ 155
Cdd:smart00431  81 EDLERELDEPGQQVSAHVHGQEVLLEKMVPL 111
SCAN cd07936
SCAN oligomerization domain; The SCAN domain (named after SRE-ZBP, CTfin51, AW-1 and Number 18 ...
 45-129 5.12e-34

SCAN oligomerization domain; The SCAN domain (named after SRE-ZBP, CTfin51, AW-1 and Number 18 cDNA) is found in several vertebrate proteins that contain C2H2 zinc finger motifs, many of which may be transcription factors playing roles in cell survival and differentiation. This protein-interaction domain is able to mediate homo- and hetero-oligomerization of SCAN-containing proteins. Some SCAN-containing proteins, including those of lower vertebrates, do not contain zinc finger motifs. It has been noted that the SCAN domain resembles a domain-swapped version of the C-terminal domain of the HIV capsid protein. This domain model features elements common to the three general groups of SCAN domains (SCAN-A1, SCAN-A2, and SCAN-B). The SCAND1 protein is truncated at the C-terminus with respect to this model, the SCAND2 protein appears to have a truncated central helix.


Pssm-ID: 153421  Cd Length: 85  Bit Score: 121.60  E-value: 5.12e-34
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297307123  45 PESACRHFWSFRYHEATGPLETISQLQKLCHQWLRPEIHSKEQILEMLVLEQFLSILPKETQNWVQKHHPQNVKQALVLV 124
Cdd:cd07936    1 PETYRQRFRAFQYQEASGPREALQRLRELCRQWLRPEIHTKEQILELLVLEQFLIILPPEVQAWVRERKPESGEEAATLA 80


                 ....*
gi 297307123 125 EFLQR 129
Cdd:cd07936   81 EDLLA 85
KRAB pfam01352
KRAB box; The KRAB domain (or Kruppel-associated box) is present in about a third of zinc ...
 139-180 2.34e-18

KRAB box; The KRAB domain (or Kruppel-associated box) is present in about a third of zinc finger proteins containing C2H2 fingers. The KRAB domain is found to be involved in protein-protein interactions. The KRAB domain is generally encoded by two exons. The regions coded by the two exons are known as KRAB-A and KRAB-B. The A box plays an important role in repression by binding to corepressors, while the B box is thought to enhance this repression brought about by the A box. KRAB-containing proteins are thought to have critical functions in cell proliferation and differentiation, apoptosis and neoplastic transformation.


Pssm-ID: 460171  Cd Length: 42  Bit Score: 77.90  E-value: 2.34e-18
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 297307123  139 LLTFEDVAVYFSEEEWQLLNPLEKTLYNDVMQDIYETVISLG 180
Cdd:pfam01352   1 SVTFEDVAVDFTQEEWALLDPAQRNLYRDVMLENYRNLVSLG 42
KRAB smart00349
krueppel associated box;
140-185 1.14e-17

krueppel associated box;


Pssm-ID: 214630 [Multi-domain]  Cd Length: 61  Bit Score: 76.48  E-value: 1.14e-17
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 297307123   140 LTFEDVAVYFSEEEWQLLNPLEKTLYNDVMQDIYETVISLGLKLKN 185
Cdd:smart00349   1 VTFEDVAVYFTQEEWEQLDPAQKNLYRDVMLENYSNLVSLGFQVPK 46
KRAB_A-box cd07765
KRAB (Kruppel-associated box) domain -A box; The KRAB domain is a transcription repression ...
 140-179 1.26e-16

KRAB (Kruppel-associated box) domain -A box; The KRAB domain is a transcription repression module, found in a subgroup of the zinc finger proteins (ZFPs) of the C2H2 family, KRAB-ZFPs. KRAB-ZFPs comprise the largest group of transcriptional regulators in mammals, and are only found in tetrapods. These proteins have been shown to play important roles in cell differentiation and organ development, and in regulating viral replication and transcription. A KRAB domain may consist of an A-box, or of an A-box plus either a B-box, a divergent B-box (b), or a C-box. Only the A-box is included in this model. The A-box is needed for repression, the B- and C- boxes are not. KRAB-ZFPs have one or two KRAB domains at their amino-terminal end, and multiple C2H2 zinc finger motifs at their C-termini. Some KRAB-ZFPs also contain a SCAN domain which mediates homo- and hetero-oligomerization. The KRAB domain is a protein-protein interaction module which represses transcription through recruiting corepressors. A key mechanism appears to be the following: KRAB-AFPs tethered to DNA recruit, via their KRAB domain, the repressor KAP1 (KRAB-associated protein-1, also known as transcription intermediary factor 1 beta , KRAB-A interacting protein , and tripartite motif protein 28). The KAP1/ KRAB-AFP complex in turn recruits the heterochromatin protein 1 (HP1) family, and other chromatin modulating proteins, leading to transcriptional repression through heterochromatin formation.


Pssm-ID: 143639  Cd Length: 40  Bit Score: 72.97  E-value: 1.26e-16
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|
gi 297307123 140 LTFEDVAVYFSEEEWQLLNPLEKTLYNDVMQDIYETVISL 179
Cdd:cd07765    1 VTFEDVAVYFSQEEWELLDPAQRDLYRDVMLENYENLVSL 40
COG5048 COG5048
FOG: Zn-finger [General function prediction only];
283-397 1.80e-05

FOG: Zn-finger [General function prediction only];


Pssm-ID: 227381 [Multi-domain]  Cd Length: 467  Bit Score: 46.61  E-value: 1.80e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297307123 283 SDLIKHHRIHTGEKPYKCQQCDRRFRWSSDLNKHFMTHQGI-KPYRCSWCGKSFSHNTNLHTHQR--IHTGE--KPFKCD 357
Cdd:COG5048  246 SSLSSSDSSSSASESPRSSLPTASSQSSSPNESDSSSEKGFsLPIKSKQCNISFSRSSPLTRHLRsvNHSGEslKPFSCP 325

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|..
gi 297307123 358 E--CGKRFIQNSHLIKHQRTHTGEQPYTCSLCKRNFSRRSSL 397
Cdd:COG5048  326 YslCGKLFSRNDALKRHILLHTSISPAKEKLLNSSSKFSPLL 367
zf-H2C2_2 pfam13465
Zinc-finger double domain;
340-365 7.59e-05

Zinc-finger double domain;


Pssm-ID: 463886 [Multi-domain]  Cd Length: 26  Bit Score: 39.28  E-value: 7.59e-05
                          10        20
                  ....*....|....*....|....*.
gi 297307123  340 NLHTHQRIHTGEKPFKCDECGKRFIQ 365
Cdd:pfam13465   1 NLKRHMRTHTGEKPYKCPECGKSFKS 26
SUF4-like cd20908
N-terminal domain of Oryza sativa transcription factor SUPPRESSOR OF FRI 4 (OsSUF4), ...
 324-372 5.86e-04

N-terminal domain of Oryza sativa transcription factor SUPPRESSOR OF FRI 4 (OsSUF4), Arabidopsis thaliana SUF4 (AtSUF4), and similar proteins; Oryza sativa SUPPRESSOR OF FRI 4 (OsSUF4) is a C2H2-type zinc finger transcription factor which interacts with the major H3K36 methyltransferase SDG725 to promote H3K36me3 (tri-methylation at H3K9) establishment. The transcription factor OsSUF4 recognizes a specific 7-bp DNA element (5'-CGGAAAT-3'), which is contained in the promoter regions of many genes throughout the rice genome. Through interaction with OsSUF4, SDG725 is recruited to the promoters of key florigen genes, RICE FLOWERING LOCUS T1 (RFT1) and Heading date 3a (Hd3a), for H3K36 deposition to promote gene activation and rice plant flowering. OsSUF4 target genes include a number of genes involved in many biological processes. Flowering plant Arabidopsis SUF4 binds to a 15bp DNA element (5'-CCAAATTTTAAGTTT-3') within the promoter of the floral repressor gene FLOWERING LOCUS C (FLC) and recruits the FRI-C transcription activator complex to the FLC promoter. Although the DNA-binding element and target genes of AtSUF4 are different from those of OsSUF4, AtSUF4 is known to interact with the Arabidopsis H3K36 methyltransferase SDG8 (also known as ASHH2/EFS/SET8), and the methylation deposition mechanism mediated by the SUF4 transcription factor and H3K36 methyltransferase may be conserved in Arabidopsis and rice. Proteins in this family have two conserved C2H2-type zinc finger motifs at the N-terminus (included in this model), and a large proline-rich domain at the C-terminus; for OsSUF4, it has been shown that the N-terminal zinc-finger domain is responsible for DNA binding, and that the C-terminal domain interacts with SDG725.


Pssm-ID: 411020 [Multi-domain]  Cd Length: 82  Bit Score: 38.31  E-value: 5.86e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 297307123 324 KPYrCSWCGKSFSHNTNLHTHQRIHTgekpFKCDECGKRFIQNSHLIKH 372
Cdd:cd20908    1 KPW-CYYCDREFDDEKILIQHQKAKH----FKCHICHKKLYTAGGLAVH 44
zf-C2H2 pfam00096
Zinc finger, C2H2 type; The C2H2 zinc finger is the classical zinc finger domain. The two ...
 270-292 7.45e-04

Zinc finger, C2H2 type; The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger. #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C] Where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter.


Pssm-ID: 395048 [Multi-domain]  Cd Length: 23  Bit Score: 36.51  E-value: 7.45e-04
                          10        20
                  ....*....|....*....|...
gi 297307123  270 FKCQECGKSFRVSSDLIKHHRIH 292
Cdd:pfam00096   1 YKCPDCGKSFSRKSNLKRHLRTH 23
 
Name Accession Description Interval E-value
SCAN pfam02023
SCAN domain; The SCAN domain (named after SRE-ZBP, CTfin51, AW-1 and Number 18 cDNA) is found ...
 45-133 1.61e-47

SCAN domain; The SCAN domain (named after SRE-ZBP, CTfin51, AW-1 and Number 18 cDNA) is found in several pfam00096 proteins. The domain has been shown to be able to mediate homo- and hetero-oligomerization.


Pssm-ID: 460417 [Multi-domain]  Cd Length: 89  Bit Score: 157.26  E-value: 1.61e-47
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297307123   45 PESACRHFWSFRYHEATGPLETISQLQKLCHQWLRPEIHSKEQILEMLVLEQFLSILPKETQNWVQKHHPQNVKQALVLV 124
Cdd:pfam02023   1 PEASRQRFRQFCYQEAEGPREALSQLRELCHQWLRPEKHTKEQILELLVLEQFLTILPEEIQSWVREHHPESGEEAVALA 80


                  ....*....
gi 297307123  125 EFLQREPDG 133
Cdd:pfam02023  81 EDLLLERGE 89
SCAN smart00431
leucine rich region;
45-155 1.76e-44

leucine rich region;


Pssm-ID: 128708 [Multi-domain]  Cd Length: 113  Bit Score: 150.15  E-value: 1.76e-44
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297307123    45 PESACRHFWSFRYHEATGPLETISQLQKLCHQWLRPEIHSKEQILEMLVLEQFLSILPKETQNWVQKHHPQNVKQALVLV 124
Cdd:smart00431   1 PEIFRQRFRQFRYQETSGPREALSRLRELCRQWLRPELHTKEQILELLVLEQFLTILPGELQAWVREHHPESGEEAVTLL 80

                           90       100       110
                   ....*....|....*....|....*....|.
gi 297307123   125 EFLQREPDGTKNESLLTFEDVAVYFSEEEWQ 155
Cdd:smart00431  81 EDLERELDEPGQQVSAHVHGQEVLLEKMVPL 111
SCAN cd07936
SCAN oligomerization domain; The SCAN domain (named after SRE-ZBP, CTfin51, AW-1 and Number 18 ...
 45-129 5.12e-34

SCAN oligomerization domain; The SCAN domain (named after SRE-ZBP, CTfin51, AW-1 and Number 18 cDNA) is found in several vertebrate proteins that contain C2H2 zinc finger motifs, many of which may be transcription factors playing roles in cell survival and differentiation. This protein-interaction domain is able to mediate homo- and hetero-oligomerization of SCAN-containing proteins. Some SCAN-containing proteins, including those of lower vertebrates, do not contain zinc finger motifs. It has been noted that the SCAN domain resembles a domain-swapped version of the C-terminal domain of the HIV capsid protein. This domain model features elements common to the three general groups of SCAN domains (SCAN-A1, SCAN-A2, and SCAN-B). The SCAND1 protein is truncated at the C-terminus with respect to this model, the SCAND2 protein appears to have a truncated central helix.


Pssm-ID: 153421  Cd Length: 85  Bit Score: 121.60  E-value: 5.12e-34
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297307123  45 PESACRHFWSFRYHEATGPLETISQLQKLCHQWLRPEIHSKEQILEMLVLEQFLSILPKETQNWVQKHHPQNVKQALVLV 124
Cdd:cd07936    1 PETYRQRFRAFQYQEASGPREALQRLRELCRQWLRPEIHTKEQILELLVLEQFLIILPPEVQAWVRERKPESGEEAATLA 80


                 ....*
gi 297307123 125 EFLQR 129
Cdd:cd07936   81 EDLLA 85
KRAB pfam01352
KRAB box; The KRAB domain (or Kruppel-associated box) is present in about a third of zinc ...
 139-180 2.34e-18

KRAB box; The KRAB domain (or Kruppel-associated box) is present in about a third of zinc finger proteins containing C2H2 fingers. The KRAB domain is found to be involved in protein-protein interactions. The KRAB domain is generally encoded by two exons. The regions coded by the two exons are known as KRAB-A and KRAB-B. The A box plays an important role in repression by binding to corepressors, while the B box is thought to enhance this repression brought about by the A box. KRAB-containing proteins are thought to have critical functions in cell proliferation and differentiation, apoptosis and neoplastic transformation.


Pssm-ID: 460171  Cd Length: 42  Bit Score: 77.90  E-value: 2.34e-18
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 297307123  139 LLTFEDVAVYFSEEEWQLLNPLEKTLYNDVMQDIYETVISLG 180
Cdd:pfam01352   1 SVTFEDVAVDFTQEEWALLDPAQRNLYRDVMLENYRNLVSLG 42
KRAB smart00349
krueppel associated box;
140-185 1.14e-17

krueppel associated box;


Pssm-ID: 214630 [Multi-domain]  Cd Length: 61  Bit Score: 76.48  E-value: 1.14e-17
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 297307123   140 LTFEDVAVYFSEEEWQLLNPLEKTLYNDVMQDIYETVISLGLKLKN 185
Cdd:smart00349   1 VTFEDVAVYFTQEEWEQLDPAQKNLYRDVMLENYSNLVSLGFQVPK 46
KRAB_A-box cd07765
KRAB (Kruppel-associated box) domain -A box; The KRAB domain is a transcription repression ...
 140-179 1.26e-16

KRAB (Kruppel-associated box) domain -A box; The KRAB domain is a transcription repression module, found in a subgroup of the zinc finger proteins (ZFPs) of the C2H2 family, KRAB-ZFPs. KRAB-ZFPs comprise the largest group of transcriptional regulators in mammals, and are only found in tetrapods. These proteins have been shown to play important roles in cell differentiation and organ development, and in regulating viral replication and transcription. A KRAB domain may consist of an A-box, or of an A-box plus either a B-box, a divergent B-box (b), or a C-box. Only the A-box is included in this model. The A-box is needed for repression, the B- and C- boxes are not. KRAB-ZFPs have one or two KRAB domains at their amino-terminal end, and multiple C2H2 zinc finger motifs at their C-termini. Some KRAB-ZFPs also contain a SCAN domain which mediates homo- and hetero-oligomerization. The KRAB domain is a protein-protein interaction module which represses transcription through recruiting corepressors. A key mechanism appears to be the following: KRAB-AFPs tethered to DNA recruit, via their KRAB domain, the repressor KAP1 (KRAB-associated protein-1, also known as transcription intermediary factor 1 beta , KRAB-A interacting protein , and tripartite motif protein 28). The KAP1/ KRAB-AFP complex in turn recruits the heterochromatin protein 1 (HP1) family, and other chromatin modulating proteins, leading to transcriptional repression through heterochromatin formation.


Pssm-ID: 143639  Cd Length: 40  Bit Score: 72.97  E-value: 1.26e-16
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|
gi 297307123 140 LTFEDVAVYFSEEEWQLLNPLEKTLYNDVMQDIYETVISL 179
Cdd:cd07765    1 VTFEDVAVYFSQEEWELLDPAQRDLYRDVMLENYENLVSL 40
COG5048 COG5048
FOG: Zn-finger [General function prediction only];
283-397 1.80e-05

FOG: Zn-finger [General function prediction only];


Pssm-ID: 227381 [Multi-domain]  Cd Length: 467  Bit Score: 46.61  E-value: 1.80e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297307123 283 SDLIKHHRIHTGEKPYKCQQCDRRFRWSSDLNKHFMTHQGI-KPYRCSWCGKSFSHNTNLHTHQR--IHTGE--KPFKCD 357
Cdd:COG5048  246 SSLSSSDSSSSASESPRSSLPTASSQSSSPNESDSSSEKGFsLPIKSKQCNISFSRSSPLTRHLRsvNHSGEslKPFSCP 325

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|..
gi 297307123 358 E--CGKRFIQNSHLIKHQRTHTGEQPYTCSLCKRNFSRRSSL 397
Cdd:COG5048  326 YslCGKLFSRNDALKRHILLHTSISPAKEKLLNSSSKFSPLL 367
COG5048 COG5048
FOG: Zn-finger [General function prediction only];
268-404 3.10e-05

FOG: Zn-finger [General function prediction only];


Pssm-ID: 227381 [Multi-domain]  Cd Length: 467  Bit Score: 45.84  E-value: 3.10e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297307123 268 KPFKCQECGKSFRVSSDLIKH--HRIHTGE--KPYKC--QQCDRRFRWSSDLNKHFMTHQGIKPYRCSWCGKSFSHNTNL 341
Cdd:COG5048  288 LPIKSKQCNISFSRSSPLTRHlrSVNHSGEslKPFSCpySLCGKLFSRNDALKRHILLHTSISPAKEKLLNSSSKFSPLL 367

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 297307123 342 -------HTHQRIHTGEKPFKCD--ECGKRFIQNSHLIKHQRTHTGEQPY--TCSLCKRNFSRRSSLLRHQKLH 404
Cdd:COG5048  368 nneppqsLQQYKDLKNDKKSETLsnSCIRNFKRDSNLSLHIITHLSFRPYncKNPPCSKSFNRHYNLIPHKKIH 441
COG5048 COG5048
FOG: Zn-finger [General function prediction only];
324-404 5.72e-05

FOG: Zn-finger [General function prediction only];


Pssm-ID: 227381 [Multi-domain]  Cd Length: 467  Bit Score: 45.07  E-value: 5.72e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297307123 324 KPYRCSWCGKSFSHNTNLHTHQRIHTGEKPFKC--DECGKRFIQNSHLIKHQRTHTGEQPYTCS--LCKRNFSRRSSLLR 399
Cdd:COG5048   32 RPDSCPNCTDSFSRLEHLTRHIRSHTGEKPSQCsySGCDKSFSRPLELSRHLRTHHNNPSDLNSksLPLSNSKASSSSLS 111


                 ....*
gi 297307123 400 HQKLH 404
Cdd:COG5048  112 SSSSN 116
zf-H2C2_2 pfam13465
Zinc-finger double domain;
340-365 7.59e-05

Zinc-finger double domain;


Pssm-ID: 463886 [Multi-domain]  Cd Length: 26  Bit Score: 39.28  E-value: 7.59e-05
                          10        20
                  ....*....|....*....|....*.
gi 297307123  340 NLHTHQRIHTGEKPFKCDECGKRFIQ 365
Cdd:pfam13465   1 NLKRHMRTHTGEKPYKCPECGKSFKS 26
zf-C2H2 pfam00096
Zinc finger, C2H2 type; The C2H2 zinc finger is the classical zinc finger domain. The two ...
 354-376 8.38e-05

Zinc finger, C2H2 type; The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger. #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C] Where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter.


Pssm-ID: 395048 [Multi-domain]  Cd Length: 23  Bit Score: 39.21  E-value: 8.38e-05
                          10        20
                  ....*....|....*....|...
gi 297307123  354 FKCDECGKRFIQNSHLIKHQRTH 376
Cdd:pfam00096   1 YKCPDCGKSFSRKSNLKRHLRTH 23
SFP1 COG5189
Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division ...
 266-344 8.87e-05

Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning];


Pssm-ID: 227516 [Multi-domain]  Cd Length: 423  Bit Score: 44.32  E-value: 8.87e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297307123 266 GEKPFKCQ--ECGKSFRvSSDLIKHHRIHTgekpykcqQCDRRFRWSSDLNKHFMTHQGIKPYRCSWCGKSFSHNTNLHT 343
Cdd:COG5189  346 DGKPYKCPveGCNKKYK-NQNGLKYHMLHG--------HQNQKLHENPSPEKMNIFSAKDKPYRCEVCDKRYKNLNGLKY 416


                 .
gi 297307123 344 H 344
Cdd:COG5189  417 H 417
SFP1 COG5189
Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division ...
 294-377 3.03e-04

Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning];


Pssm-ID: 227516 [Multi-domain]  Cd Length: 423  Bit Score: 42.78  E-value: 3.03e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297307123 294 GEKPYKCQ--QCDRRFRWSSDLNKHfMTHqgikpyrcSWCGKSFSHNTNLHTHQRIHTGEKPFKCDECGKRFiQNSHLIK 371
Cdd:COG5189  346 DGKPYKCPveGCNKKYKNQNGLKYH-MLH--------GHQNQKLHENPSPEKMNIFSAKDKPYRCEVCDKRY-KNLNGLK 415


                 ....*.
gi 297307123 372 HQRTHT 377
Cdd:COG5189  416 YHRKHS 421
zf-H2C2_2 pfam13465
Zinc-finger double domain;
284-307 4.48e-04

Zinc-finger double domain;


Pssm-ID: 463886 [Multi-domain]  Cd Length: 26  Bit Score: 37.35  E-value: 4.48e-04
                          10        20
                  ....*....|....*....|....
gi 297307123  284 DLIKHHRIHTGEKPYKCQQCDRRF 307
Cdd:pfam13465   1 NLKRHMRTHTGEKPYKCPECGKSF 24
SUF4-like cd20908
N-terminal domain of Oryza sativa transcription factor SUPPRESSOR OF FRI 4 (OsSUF4), ...
 324-372 5.86e-04

N-terminal domain of Oryza sativa transcription factor SUPPRESSOR OF FRI 4 (OsSUF4), Arabidopsis thaliana SUF4 (AtSUF4), and similar proteins; Oryza sativa SUPPRESSOR OF FRI 4 (OsSUF4) is a C2H2-type zinc finger transcription factor which interacts with the major H3K36 methyltransferase SDG725 to promote H3K36me3 (tri-methylation at H3K9) establishment. The transcription factor OsSUF4 recognizes a specific 7-bp DNA element (5'-CGGAAAT-3'), which is contained in the promoter regions of many genes throughout the rice genome. Through interaction with OsSUF4, SDG725 is recruited to the promoters of key florigen genes, RICE FLOWERING LOCUS T1 (RFT1) and Heading date 3a (Hd3a), for H3K36 deposition to promote gene activation and rice plant flowering. OsSUF4 target genes include a number of genes involved in many biological processes. Flowering plant Arabidopsis SUF4 binds to a 15bp DNA element (5'-CCAAATTTTAAGTTT-3') within the promoter of the floral repressor gene FLOWERING LOCUS C (FLC) and recruits the FRI-C transcription activator complex to the FLC promoter. Although the DNA-binding element and target genes of AtSUF4 are different from those of OsSUF4, AtSUF4 is known to interact with the Arabidopsis H3K36 methyltransferase SDG8 (also known as ASHH2/EFS/SET8), and the methylation deposition mechanism mediated by the SUF4 transcription factor and H3K36 methyltransferase may be conserved in Arabidopsis and rice. Proteins in this family have two conserved C2H2-type zinc finger motifs at the N-terminus (included in this model), and a large proline-rich domain at the C-terminus; for OsSUF4, it has been shown that the N-terminal zinc-finger domain is responsible for DNA binding, and that the C-terminal domain interacts with SDG725.


Pssm-ID: 411020 [Multi-domain]  Cd Length: 82  Bit Score: 38.31  E-value: 5.86e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 297307123 324 KPYrCSWCGKSFSHNTNLHTHQRIHTgekpFKCDECGKRFIQNSHLIKH 372
Cdd:cd20908    1 KPW-CYYCDREFDDEKILIQHQKAKH----FKCHICHKKLYTAGGLAVH 44
zf-C2H2 pfam00096
Zinc finger, C2H2 type; The C2H2 zinc finger is the classical zinc finger domain. The two ...
 270-292 7.45e-04

Zinc finger, C2H2 type; The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger. #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C] Where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter.


Pssm-ID: 395048 [Multi-domain]  Cd Length: 23  Bit Score: 36.51  E-value: 7.45e-04
                          10        20
                  ....*....|....*....|...
gi 297307123  270 FKCQECGKSFRVSSDLIKHHRIH 292
Cdd:pfam00096   1 YKCPDCGKSFSRKSNLKRHLRTH 23
zf-C2H2 pfam00096
Zinc finger, C2H2 type; The C2H2 zinc finger is the classical zinc finger domain. The two ...
 326-348 7.45e-04

Zinc finger, C2H2 type; The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger. #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C] Where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter.


Pssm-ID: 395048 [Multi-domain]  Cd Length: 23  Bit Score: 36.51  E-value: 7.45e-04
                          10        20
                  ....*....|....*....|...
gi 297307123  326 YRCSWCGKSFSHNTNLHTHQRIH 348
Cdd:pfam00096   1 YKCPDCGKSFSRKSNLKRHLRTH 23
zf-C2H2 pfam00096
Zinc finger, C2H2 type; The C2H2 zinc finger is the classical zinc finger domain. The two ...
 382-404 9.64e-03

Zinc finger, C2H2 type; The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger. #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C] Where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter.


Pssm-ID: 395048 [Multi-domain]  Cd Length: 23  Bit Score: 33.43  E-value: 9.64e-03
                          10        20
                  ....*....|....*....|...
gi 297307123  382 YTCSLCKRNFSRRSSLLRHQKLH 404
Cdd:pfam00096   1 YKCPDCGKSFSRKSNLKRHLRTH 23
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH