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Conserved domains on  [gi|1743125241|pdb|6KIW|A]
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Chain A, Histone H3

Protein Classification

histone H3( domain architecture ID 10794185)

histone H3 is a core component of the nucleosome that wraps and compacts DNA into chromatin, limiting DNA accessibility to the cellular machineries which require DNA as a template

CATH:  1.10.20.10
Gene Ontology:  GO:0003677|GO:0046982|GO:0030527
PubMed:  8121801|33155135

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PTZ00018 PTZ00018
histone H3; Provisional
 1-135 1.64e-87

histone H3; Provisional


:

Pssm-ID: 185400 [Multi-domain]  Cd Length: 136  Bit Score: 250.59  E-value: 1.64e-87
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
6KIW_A         1 ARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKT 80
Cdd:PTZ00018   2 ARTKQTARKSTGGKAPRKQLASKAARKSAPVTGGIKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKT 81

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*
6KIW_A        81 DLRFQSSAVMALQEASEAYLVALFEDTNLCAIHAKRVTIMPKDIQLARRIRGERA 135
Cdd:PTZ00018  82 DLRFQSSAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGERS 136
 
Name Accession Description Interval E-value
PTZ00018 PTZ00018
histone H3; Provisional
 1-135 1.64e-87

histone H3; Provisional


Pssm-ID: 185400 [Multi-domain]  Cd Length: 136  Bit Score: 250.59  E-value: 1.64e-87
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
6KIW_A         1 ARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKT 80
Cdd:PTZ00018   2 ARTKQTARKSTGGKAPRKQLASKAARKSAPVTGGIKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKT 81

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*
6KIW_A        81 DLRFQSSAVMALQEASEAYLVALFEDTNLCAIHAKRVTIMPKDIQLARRIRGERA 135
Cdd:PTZ00018  82 DLRFQSSAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGERS 136
HFD_H3 cd22911
histone-fold domain found in histone H3 and similar proteins; Histone H3 is a core component ...
 39-132 1.04e-62

histone-fold domain found in histone H3 and similar proteins; Histone H3 is a core component of the nucleosome, which wraps and compacts DNA into chromatin, limiting DNA accessibility to the cellular machineries which require DNA as a template. Histones thereby play a central role in transcription regulation, DNA repair, DNA replication, and chromosomal stability. DNA accessibility is regulated via a complex set of post-translational modifications of histones, also called the histone code, and nucleosome remodeling. The nucleosome is a histone octamer containing two molecules each of H2A, H2B, H3 and H4 assembled in one H3-H4 heterotetramer and two H2A-H2B heterodimers. The octamer wraps approximately 147 bp of DNA.


Pssm-ID: 467036  Cd Length: 95  Bit Score: 186.59  E-value: 1.04e-62
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
6KIW_A       39 HRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKT-DLRFQSSAVMALQEASEAYLVALFEDTNLCAIHAKRV 117
Cdd:cd22911   1 RRYRPGTVALREIRRYQKSTELLIPKLPFQRLVREIAQDFKTkDLRFQSSALLALQEAAEAYLVGLFEDSNLCAIHAKRV 80

                        90
                ....*....|....*
6KIW_A      118 TIMPKDIQLARRIRG 132
Cdd:cd22911  81 TLMPKDMQLARRIRG 95
H3 smart00428
Histone H3;
33-135 3.90e-60

Histone H3;


Pssm-ID: 128705 [Multi-domain]  Cd Length: 105  Bit Score: 180.34  E-value: 3.90e-60
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
6KIW_A          33 GGVKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKT--DLRFQSSAVMALQEASEAYLVALFEDTNLC 110
Cdd:smart00428   1 GGKTKHRRYRPGQVALREIRKYQKSTDLLIRKAPFQRLVREIAQKFTTgvDLRFQSSAIMALQEAAEAYLVGLFEDTNLL 80

                           90       100
                   ....*....|....*....|....*
6KIW_A         111 AIHAKRVTIMPKDIQLARRIRGERA 135
Cdd:smart00428  81 AIHAKRVTIMPKDIQLARRIRGERL 105
Histone pfam00125
Core histone H2A/H2B/H3/H4;
1-131 2.57e-50

Core histone H2A/H2B/H3/H4;


Pssm-ID: 459682 [Multi-domain]  Cd Length: 126  Bit Score: 156.44  E-value: 2.57e-50
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
6KIW_A          1 ARTKQTARKSTGGKAPRKQLATKAARKSapatggVKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKT 80
Cdd:pfam00125   2 ARNKNKANPRRGGTAPEKKISQKSSSSS------KKKTRRYRPGTVALKEIRKYQSSTDLLIYKLPFARVVREVVQSTKT 75

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|.
6KIW_A         81 DLRFQSSAVMALQEASEAYLVALFEDTNLCAIHAKRVTIMPKDIQLARRIR 131
Cdd:pfam00125  76 DLRISADAVVALQEAVEDFLVELFEEANLLAIHAKRVTLTPKDIQLARRLR 126
 
Name Accession Description Interval E-value
PTZ00018 PTZ00018
histone H3; Provisional
 1-135 1.64e-87

histone H3; Provisional


Pssm-ID: 185400 [Multi-domain]  Cd Length: 136  Bit Score: 250.59  E-value: 1.64e-87
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
6KIW_A         1 ARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKT 80
Cdd:PTZ00018   2 ARTKQTARKSTGGKAPRKQLASKAARKSAPVTGGIKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKT 81

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*
6KIW_A        81 DLRFQSSAVMALQEASEAYLVALFEDTNLCAIHAKRVTIMPKDIQLARRIRGERA 135
Cdd:PTZ00018  82 DLRFQSSAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGERS 136
PLN00121 PLN00121
histone H3; Provisional
 1-135 4.27e-80

histone H3; Provisional


Pssm-ID: 177733 [Multi-domain]  Cd Length: 136  Bit Score: 232.25  E-value: 4.27e-80
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
6KIW_A         1 ARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKT 80
Cdd:PLN00121   2 ARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRKYQKSTELLIRKLPFQRLVREIAQDFKT 81

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*
6KIW_A        81 DLRFQSSAVMALQEASEAYLVALFEDTNLCAIHAKRVTIMPKDIQLARRIRGERA 135
Cdd:PLN00121  82 DLRFQSSAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGERA 136
HFD_H3 cd22911
histone-fold domain found in histone H3 and similar proteins; Histone H3 is a core component ...
 39-132 1.04e-62

histone-fold domain found in histone H3 and similar proteins; Histone H3 is a core component of the nucleosome, which wraps and compacts DNA into chromatin, limiting DNA accessibility to the cellular machineries which require DNA as a template. Histones thereby play a central role in transcription regulation, DNA repair, DNA replication, and chromosomal stability. DNA accessibility is regulated via a complex set of post-translational modifications of histones, also called the histone code, and nucleosome remodeling. The nucleosome is a histone octamer containing two molecules each of H2A, H2B, H3 and H4 assembled in one H3-H4 heterotetramer and two H2A-H2B heterodimers. The octamer wraps approximately 147 bp of DNA.


Pssm-ID: 467036  Cd Length: 95  Bit Score: 186.59  E-value: 1.04e-62
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
6KIW_A       39 HRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKT-DLRFQSSAVMALQEASEAYLVALFEDTNLCAIHAKRV 117
Cdd:cd22911   1 RRYRPGTVALREIRRYQKSTELLIPKLPFQRLVREIAQDFKTkDLRFQSSALLALQEAAEAYLVGLFEDSNLCAIHAKRV 80

                        90
                ....*....|....*
6KIW_A      118 TIMPKDIQLARRIRG 132
Cdd:cd22911  81 TLMPKDMQLARRIRG 95
H3 smart00428
Histone H3;
33-135 3.90e-60

Histone H3;


Pssm-ID: 128705 [Multi-domain]  Cd Length: 105  Bit Score: 180.34  E-value: 3.90e-60
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
6KIW_A          33 GGVKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKT--DLRFQSSAVMALQEASEAYLVALFEDTNLC 110
Cdd:smart00428   1 GGKTKHRRYRPGQVALREIRKYQKSTDLLIRKAPFQRLVREIAQKFTTgvDLRFQSSAIMALQEAAEAYLVGLFEDTNLL 80

                           90       100
                   ....*....|....*....|....*
6KIW_A         111 AIHAKRVTIMPKDIQLARRIRGERA 135
Cdd:smart00428  81 AIHAKRVTIMPKDIQLARRIRGERL 105
Histone pfam00125
Core histone H2A/H2B/H3/H4;
1-131 2.57e-50

Core histone H2A/H2B/H3/H4;


Pssm-ID: 459682 [Multi-domain]  Cd Length: 126  Bit Score: 156.44  E-value: 2.57e-50
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
6KIW_A          1 ARTKQTARKSTGGKAPRKQLATKAARKSapatggVKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKT 80
Cdd:pfam00125   2 ARNKNKANPRRGGTAPEKKISQKSSSSS------KKKTRRYRPGTVALKEIRKYQSSTDLLIYKLPFARVVREVVQSTKT 75

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|.
6KIW_A         81 DLRFQSSAVMALQEASEAYLVALFEDTNLCAIHAKRVTIMPKDIQLARRIR 131
Cdd:pfam00125  76 DLRISADAVVALQEAVEDFLVELFEEANLLAIHAKRVTLTPKDIQLARRLR 126
PLN00161 PLN00161
histone H3; Provisional
 1-132 1.96e-46

histone H3; Provisional


Pssm-ID: 215082 [Multi-domain]  Cd Length: 135  Bit Score: 146.68  E-value: 1.96e-46
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
6KIW_A         1 ARTKQtARKSTGGKAPRKQLATKAARKSApatggvKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKT 80
Cdd:PLN00161   2 ARRLQ-GKRFRKGKKPQKEASGVTRQELD------KKPHRYRPGTVALREIRKYQKSTELLIRKLPFARLVREISNEMLR 74

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|...
6KIW_A        81 D-LRFQSSAVMALQEASEAYLVALFEDTNLCAIHAKRVTIMPKDIQLARRIRG 132
Cdd:PLN00161  75 EpFRWTAEALLALQEATEDFLVHLFEDCNLCAIHAKRVTIMPKDMQLARRIRG 127
PLN00160 PLN00160
histone H3; Provisional
 42-133 3.12e-38

histone H3; Provisional


Pssm-ID: 165727  Cd Length: 97  Bit Score: 124.77  E-value: 3.12e-38
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
6KIW_A        42 RPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDF-KTDLRFQSSAVMALQEASEAYLVALFEDTNLCAIHAKRVTIM 120
Cdd:PLN00160   2 RPGEKALKEIKMYQKSTDLLIRRLPFARLVREIQMEMsREAYRWQGSAILALQEAAEAHLVGLFEDSNLCAIHGKRVTIM 81

                         90
                 ....*....|...
6KIW_A       121 PKDIQLARRIRGE 133
Cdd:PLN00160  82 PKDMQLARRIRGQ 94
HFD_CENP-T cd22920
histone-fold domain found in centromere protein T (CENP-T) and similar proteins; CENP-T, also ...
 69-131 1.18e-04

histone-fold domain found in centromere protein T (CENP-T) and similar proteins; CENP-T, also called interphase centromere complex protein 22 (ICEN22), is a component of the CENPA-NAC (nucleosome-associated) complex, which plays a central role in the assembly of kinetochore proteins, mitotic progression, and chromosome segregation. The CENPA-NAC complex recruits the CENPA-CAD (nucleosome distal) complex and may be involved in incorporation of newly synthesized CENPA into centromeres. CENP-T is also part of a nucleosome-associated complex that binds specifically to histone H3-containing nucleosomes at the centromere, as opposed to nucleosomes containing CENPA. Moreover, CENP-T is a component of the heterotetrameric CENP-T-W-S-X complex that binds and supercoils DNA, and plays an important role in kinetochore assembly. CENP-T has a fundamental role in kinetochore assembly and function. It is one of the inner kinetochore proteins, with most further proteins binding downstream. It is required for normal chromosome organization and normal progress through mitosis.


Pssm-ID: 467045  Cd Length: 94  Bit Score: 38.69  E-value: 1.18e-04
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....
6KIW_A       69 RLVREIAQdFKTDLRFQSSAVMALQEASEAYLVALFEDTNLCAIHAKRVTIMPKD-IQLARRIR 131
Cdd:cd22920   6 SLVKKLFK-HFLKRRVSKEALEALEEISEEFFEQLSDDLEAYADHAGRKTINEKDvELLMKRQR 68
HFD_SF cd00076
histone fold domain (HFD) superfamily; The histone fold domain (HFD) is a structurally ...
 67-127 4.01e-04

histone fold domain (HFD) superfamily; The histone fold domain (HFD) is a structurally conserved interaction motif involved in heterodimerization of the core histones and their assembly into the nucleosome octamer. Histone fold heterodimers play crucial roles in gene regulation. The minimal HFD consists of three alpha helices connected by two short, unstructured loops. The HFD is found in core histones, TATA box-binding protein-associated factors (TAFs), and many other transcription factors. HFD plays a role in the nucleosomal core particle by conserving histone interactions; these contain more than one HFD. The structure of the nucleosome core particle has two modes that have the largest interaction surfaces, and these are the H3-H4 and H2A-H2B heterodimer interactions. Several TAFs interact via histone-fold (HF) motifs. Five HF-containing TAF pairs have been described in transcription factor II D (TFIID): TAF6-TAF9, TAF4-TAF12, TAF11-TAF13, TAF8-TAF10 and TAF3-TAF10.


Pssm-ID: 467021  Cd Length: 63  Bit Score: 36.43  E-value: 4.01e-04
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|.
6KIW_A       67 FQRLVREIAQDFKTDlRFQSSAVMALQEASEAYLVALFEDTNLCAIHAKRVTIMPKDIQLA 127
Cdd:cd00076   2 LRSAVARILKSAGFD-SVSKSALELLSDLLERYLEELARAAKAYAELAGRTTPNAEDVELA 61
 
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.
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