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Conserved domains on  [gi|30688804|ref|NP_851060|]
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nuclear factor Y, subunit B13 [Arabidopsis thaliana]

Protein Classification

histone H3/H4 domain-containing protein( domain architecture ID 581047)

histone H3/H4 domain-containing protein

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
HFD_Dr1 cd22905
histone-fold domain found in protein Dr1 and similar proteins; Dr1, also called down-regulator ...
 11-140 2.60e-61

histone-fold domain found in protein Dr1 and similar proteins; Dr1, also called down-regulator of transcription 1 or negative cofactor 2-beta (NC2-beta), is a TATA-binding protein-associated phosphoprotein and inhibitor of class II gene transcription. It forms a heterodimer with DRAP1. The association of the Dr1/DRAP1 heterodimer with TBP results in functional repression of both activated and basal transcription of class II genes. Dr1 can bind to DNA on its own. Dr1 is a component of the ADA2A-containing complex (ATAC) that has histone acetyltransferase activity on histones H3 and H4.


:

Pssm-ID: 467030  Cd Length: 129  Bit Score: 185.08  E-value: 2.60e-61
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30688804  11 KEDASLPKATMTKIIKEMLPPDVRVARDAQDLLIECCVEFINLVSSESNDVCNKEDKRTIAPEHVLKALQVLGFGEYIEE 90
Cdd:cd22905   1 DDDLSLPKATVNKLIKEVLPPDMRVSKDTRELILECCTEFIHLISSEANEICEKEKKKTISPEHVLKALENLGFGEYIEE 80

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|
gi 30688804  91 VYAAYEQHKYETMQDTQRSVKWNpGAQMTEEEAAAEQQRMFAEARARMNG 140
Cdd:cd22905  81 VEEALEDHKEEAKKRPKKSNKLK-KSGLTEEELLREQQELFAQARERQES 129
 
Name Accession Description Interval E-value
HFD_Dr1 cd22905
histone-fold domain found in protein Dr1 and similar proteins; Dr1, also called down-regulator ...
 11-140 2.60e-61

histone-fold domain found in protein Dr1 and similar proteins; Dr1, also called down-regulator of transcription 1 or negative cofactor 2-beta (NC2-beta), is a TATA-binding protein-associated phosphoprotein and inhibitor of class II gene transcription. It forms a heterodimer with DRAP1. The association of the Dr1/DRAP1 heterodimer with TBP results in functional repression of both activated and basal transcription of class II genes. Dr1 can bind to DNA on its own. Dr1 is a component of the ADA2A-containing complex (ATAC) that has histone acetyltransferase activity on histones H3 and H4.


Pssm-ID: 467030  Cd Length: 129  Bit Score: 185.08  E-value: 2.60e-61
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30688804  11 KEDASLPKATMTKIIKEMLPPDVRVARDAQDLLIECCVEFINLVSSESNDVCNKEDKRTIAPEHVLKALQVLGFGEYIEE 90
Cdd:cd22905   1 DDDLSLPKATVNKLIKEVLPPDMRVSKDTRELILECCTEFIHLISSEANEICEKEKKKTISPEHVLKALENLGFGEYIEE 80

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|
gi 30688804  91 VYAAYEQHKYETMQDTQRSVKWNpGAQMTEEEAAAEQQRMFAEARARMNG 140
Cdd:cd22905  81 VEEALEDHKEEAKKRPKKSNKLK-KSGLTEEELLREQQELFAQARERQES 129
COG5150 COG5150
Class 2 transcription repressor NC2, beta subunit (Dr1) [Transcription];
8-139 4.62e-35

Class 2 transcription repressor NC2, beta subunit (Dr1) [Transcription];


Pssm-ID: 227479  Cd Length: 148  Bit Score: 119.30  E-value: 4.62e-35
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30688804   8 GKSKEDASLPKATMTKIIKEMLPPDVRVARDAQDLLIECCVEFINLVSSESNDVCNKEDKRTIAPEHVLKALQVLGFGEY 87
Cdd:COG5150   4 EKNDDENSLPKATVQKMVSSILPKDLVFTKEAREIFINACIEFINMLSSEANEACEEEAKKTIAYEHVIKALENLEFEEY 83

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|..
gi 30688804  88 IEEVYAAYEQHKYETMQDTQRSVKWNPGAqMTEEEAAAEQQRMFAEARARMN 139
Cdd:COG5150  84 IESCMEEHENYKSYQKQKESKISKFKDSG-LSMEELLRQQEELFQNARLRFE 134
CBFD_NFYB_HMF pfam00808
Histone-like transcription factor (CBF/NF-Y) and archaeal histone; This family includes ...
 14-79 3.41e-21

Histone-like transcription factor (CBF/NF-Y) and archaeal histone; This family includes archaebacterial histones and histone like transcription factors from eukaryotes.


Pssm-ID: 395650  Cd Length: 65  Bit Score: 81.12  E-value: 3.41e-21
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 30688804    14 ASLPKATMTKIIKEMlPPDVRVARDAQDLLIECCVEFINLVSSESNDVCNKEDKRTIAPEHVLKAL 79
Cdd:pfam00808   1 AELPIARVKRIMKSD-PDAGRISQDAKELIAECVEEFIEFVASEAAEICNKAGRKTINPEHIKQAV 65
 
Name Accession Description Interval E-value
HFD_Dr1 cd22905
histone-fold domain found in protein Dr1 and similar proteins; Dr1, also called down-regulator ...
 11-140 2.60e-61

histone-fold domain found in protein Dr1 and similar proteins; Dr1, also called down-regulator of transcription 1 or negative cofactor 2-beta (NC2-beta), is a TATA-binding protein-associated phosphoprotein and inhibitor of class II gene transcription. It forms a heterodimer with DRAP1. The association of the Dr1/DRAP1 heterodimer with TBP results in functional repression of both activated and basal transcription of class II genes. Dr1 can bind to DNA on its own. Dr1 is a component of the ADA2A-containing complex (ATAC) that has histone acetyltransferase activity on histones H3 and H4.


Pssm-ID: 467030  Cd Length: 129  Bit Score: 185.08  E-value: 2.60e-61
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30688804  11 KEDASLPKATMTKIIKEMLPPDVRVARDAQDLLIECCVEFINLVSSESNDVCNKEDKRTIAPEHVLKALQVLGFGEYIEE 90
Cdd:cd22905   1 DDDLSLPKATVNKLIKEVLPPDMRVSKDTRELILECCTEFIHLISSEANEICEKEKKKTISPEHVLKALENLGFGEYIEE 80

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|
gi 30688804  91 VYAAYEQHKYETMQDTQRSVKWNpGAQMTEEEAAAEQQRMFAEARARMNG 140
Cdd:cd22905  81 VEEALEDHKEEAKKRPKKSNKLK-KSGLTEEELLREQQELFAQARERQES 129
COG5150 COG5150
Class 2 transcription repressor NC2, beta subunit (Dr1) [Transcription];
8-139 4.62e-35

Class 2 transcription repressor NC2, beta subunit (Dr1) [Transcription];


Pssm-ID: 227479  Cd Length: 148  Bit Score: 119.30  E-value: 4.62e-35
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30688804   8 GKSKEDASLPKATMTKIIKEMLPPDVRVARDAQDLLIECCVEFINLVSSESNDVCNKEDKRTIAPEHVLKALQVLGFGEY 87
Cdd:COG5150   4 EKNDDENSLPKATVQKMVSSILPKDLVFTKEAREIFINACIEFINMLSSEANEACEEEAKKTIAYEHVIKALENLEFEEY 83

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|..
gi 30688804  88 IEEVYAAYEQHKYETMQDTQRSVKWNPGAqMTEEEAAAEQQRMFAEARARMN 139
Cdd:COG5150  84 IESCMEEHENYKSYQKQKESKISKFKDSG-LSMEELLRQQEELFQNARLRFE 134
HFD_NFYB cd22907
histone-fold domain found in nuclear transcription factor Y subunit beta (NF-YB) and similar ...
 11-89 4.46e-25

histone-fold domain found in nuclear transcription factor Y subunit beta (NF-YB) and similar proteins; NF-YB, also called CAAT box DNA-binding protein subunit B, or nuclear transcription factor Y subunit B, is a component of the sequence-specific heterotrimeric transcription factor (NF-Y), which specifically recognizes the 5'-CCAAT-3' box motif found in the promoters of its target genes. NF-Y can function as both an activator and a repressor, depending on its interacting cofactors. NF-Y is a heterotrimeric transcription factor composed of three components, NF-YA, NF-YB and NF-YC. NF-YB and NF-YC must interact and dimerize for NF-YA association and DNA binding.


Pssm-ID: 467032  Cd Length: 91  Bit Score: 91.85  E-value: 4.46e-25
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 30688804  11 KEDASLPKATMTKIIKEMLPPDVRVARDAQDLLIECCVEFINLVSSESNDVCNKEDKRTIAPEHVLKALQVLGFGEYIE 89
Cdd:cd22907   3 EQDRLLPIANIARIMKKALPPNAKISKDAKETMQECVSEFISFVTSEASERCQREKRKTITGDDILWAMSTLGFDNYVE 81
HFD_POLE3_DPB4 cd22928
histone-fold domain found in DNA polymerase epsilon subunit 3 (POLE3) and similar proteins; ...
 12-98 8.98e-24

histone-fold domain found in DNA polymerase epsilon subunit 3 (POLE3) and similar proteins; POLE3, also called arsenic-transactivated protein (AsTP), chromatin accessibility complex 17 kDa protein (CHRAC-17), DNA polymerase II subunit 3, or DNA polymerase epsilon subunit p17, may participate in DNA repair and in chromosomal DNA replication. It is an accessory component of the DNA polymerase epsilon complex, which consists of four subunits: the catalytic subunit POLE and the accessory subunits POLE2, POLE3 and POLE4. It forms a complex with CHRAC1 and binds naked DNA, which is then incorporated into chromatin, aided by the nucleosome-remodeling activity of ISWI/SNF2H and ACF1. In fungi, POLE3 has been named as DNA polymerase epsilon subunit D (DPB4, also known as DNA polymerase II subunit D). DPB4 acts as an accessory component of the DNA polymerase epsilon (DNA polymerase II) that consists of POL2, DPB2, DPB3 and DPB4, and participates in chromosomal DNA replication. It also functions as a component of the ISW2 complex, which acts in remodeling the chromatin by catalyzing an ATP-dependent alteration in the structure of nucleosomal DNA.


Pssm-ID: 467053  Cd Length: 87  Bit Score: 88.34  E-value: 8.98e-24
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30688804  12 EDASLPKATMTKIIKEMLPPDVRVARDAQDLLIECCVEFINLVSSESNDVCNKEDKRTIAPEHVLKALQVLGFGEYIEEV 91
Cdd:cd22928   1 DDLELPRAVITRIIKEALPEGVQVSKDARLALSRAATVFILYLTAAANEIAKSNKRKTISADDVLKALEELEFDEFVPPL 80


                ....*..
gi 30688804  92 YAAYEQH 98
Cdd:cd22928  81 KEELEAY 87
CBFD_NFYB_HMF pfam00808
Histone-like transcription factor (CBF/NF-Y) and archaeal histone; This family includes ...
 14-79 3.41e-21

Histone-like transcription factor (CBF/NF-Y) and archaeal histone; This family includes archaebacterial histones and histone like transcription factors from eukaryotes.


Pssm-ID: 395650  Cd Length: 65  Bit Score: 81.12  E-value: 3.41e-21
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 30688804    14 ASLPKATMTKIIKEMlPPDVRVARDAQDLLIECCVEFINLVSSESNDVCNKEDKRTIAPEHVLKAL 79
Cdd:pfam00808   1 AELPIARVKRIMKSD-PDAGRISQDAKELIAECVEEFIEFVASEAAEICNKAGRKTINPEHIKQAV 65
HFD_CENP-W cd13732
histone-fold domain found in centromere protein W (CENP-W) and similar proteins; CENP-W, also ...
 17-82 5.07e-05

histone-fold domain found in centromere protein W (CENP-W) and similar proteins; CENP-W, also called cancer-up-regulated gene 2 protein (CUG2), 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 CENP-A into centromeres. CENP-W is also part of a nucleosome-associated complex that binds specifically to histone H3-containing nucleosomes at the centromere, as opposed to nucleosomes containing CENP-A. Moreover, CENP-W forms a heterodimer with CENP-T. This dimer co-assembles with CENP-S-CENP-X heterodimers at centromeres to form the tetrameric CENP-T-W-S-X complex, which is a subcomplex of the large constitutive centromere-associated network (CCAN, also known as the interphase centromere complex or ICEN). The heterotetrameric CENP-T-W-S-X complex binds and supercoils DNA and plays an important role in kinetochore assembly. CENP-W 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: 467029  Cd Length: 74  Bit Score: 39.51  E-value: 5.07e-05
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 30688804  17 PKATMTKIIKEMLPpDVRVARDAqDLLIEC-CVEFINLVSSESNDVCNKEDKRTIAPEHVLKALQVL 82
Cdd:cd13732   4 PRSTLKKIIKKHLP-GLRLAKNA-DILVYLdYLLFLQRLAEEARTEARESGSKTIKPEHVRKAAKKV 68
HFD_SF cd00076
histone fold domain (HFD) superfamily; The histone fold domain (HFD) is a structurally ...
 16-80 2.04e-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: 37.58  E-value: 2.04e-04
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 30688804  16 LPKATMTKIIKEMlpPDVRVARDAQDLLIECCVEFINLVSSESNDVCNKEDKRTIAPEHVLKALQ 80
Cdd:cd00076   1 LLRSAVARILKSA--GFDSVSKSALELLSDLLERYLEELARAAKAYAELAGRTTPNAEDVELALE 63
HFD_archaea_histone-like cd22909
histone-fold domain mainly found in archaeal histone-fold proteins, histone-like transcription ...
 16-79 3.18e-03

histone-fold domain mainly found in archaeal histone-fold proteins, histone-like transcription regulators and similar proteins; The family includes many archaeal histone-fold proteins and histone-like transcription regulators, which may bind and compact DNA (95 to 150 base pairs) to form nucleosome-like structures that contain positive DNA supercoils. They can increase the resistance of DNA to thermal denaturation.


Pssm-ID: 467034  Cd Length: 64  Bit Score: 34.44  E-value: 3.18e-03
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 30688804  16 LPKATMTKIIKEMlpPDVRVARDAQDLLIECCVEFINLVSSESNDVCNKEDKRTIAPEHVLKAL 79
Cdd:cd22909   2 LPKAPVKRIIKKA--GAERVSEDAAEELAKLLEEIAEEIAEEAVKLAKHAGRKTVKAEDIELAV 63
 
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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