SUPERFAMILY 1.75 HMM library and genome assignments server


Histone-fold superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   All alpha proteins [ 46456] (284)
Fold:   Histone-fold [ 47112]
Superfamily:   Histone-fold [ 47113] (4)
Families:   Nucleosome core histones [ 47114] (5)
  Archaeal histone [ 47129]
  TBP-associated factors, TAFs [ 47134] (13)
  Bacterial histone-fold protein [ 101318] (2)


Superfamily statistics
Genomes (644) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 26,652 39,243 82
Proteins 26,255 38,669 81


Functional annotation
General category Regulation
Detailed category DNA-binding

Document:
Function annotation of SCOP domain superfamilies

Gene Ontology (high-quality)

(show details)
GO termFDR (singleton)FDR (all)SDFO levelAnnotation (direct or inherited)
Biological Process (BP)cellular aromatic compound metabolic process7.571e-090Least InformativeDirect
Biological Process (BP)nitrogen compound metabolic process1.373e-059.966e-11Least InformativeDirect
Biological Process (BP)cellular macromolecule metabolic process1.872e-084.219e-09Least InformativeDirect
Biological Process (BP)heterocycle metabolic process5.912e-090Least InformativeDirect
Biological Process (BP)cellular component organization or biogenesis1.305e-129.174e-10Least InformativeDirect
Biological Process (BP)organic cyclic compound metabolic process1.774e-071.611e-13Least InformativeDirect
Biological Process (BP)regulation of metabolic process0.18750.0002179Least InformativeInherited
Biological Process (BP)response to stimulus0.15431Least InformativeInherited
Biological Process (BP)localization11Least InformativeInherited
Biological Process (BP)regulation of cellular process0.93480.7212Least InformativeInherited
Biological Process (BP)protein metabolic process11Least InformativeInherited
Biological Process (BP)biosynthetic process0.92856.747e-05Least InformativeInherited
Biological Process (BP)single-organism cellular process2.866e-060.1174Least InformativeInherited
Biological Process (BP)organelle organization00Moderately InformativeDirect
Biological Process (BP)regulation of biosynthetic process0.00020621.325e-07Moderately InformativeDirect
Biological Process (BP)regulation of nucleobase-containing compound metabolic process0.00028772.737e-12Moderately InformativeDirect
Biological Process (BP)macromolecular complex subunit organization0.00010541.354e-10Moderately InformativeDirect
Biological Process (BP)cellular component biogenesis0.03330.0005522Moderately InformativeInherited
Biological Process (BP)multi-organism process0.015540.2012Moderately InformativeInherited
Biological Process (BP)macromolecule localization0.81181Moderately InformativeInherited
Biological Process (BP)cellular localization11Moderately InformativeInherited
Biological Process (BP)cellular response to stress0.00026650.03142Moderately InformativeInherited
Biological Process (BP)immune system process0.44691Moderately InformativeInherited
Biological Process (BP)cellular protein modification process0.56351Moderately InformativeInherited
Biological Process (BP)RNA metabolic process0.86711.372e-07Moderately InformativeInherited
Biological Process (BP)cellular macromolecule biosynthetic process0.0096040Moderately InformativeInherited
Biological Process (BP)gene expression0.89055.895e-07Moderately InformativeInherited
Biological Process (BP)heterocycle biosynthetic process0.88471.494e-10Moderately InformativeInherited
Biological Process (BP)aromatic compound biosynthetic process0.72929.596e-11Moderately InformativeInherited
Biological Process (BP)cellular nitrogen compound biosynthetic process0.83035.005e-11Moderately InformativeInherited
Biological Process (BP)organic cyclic compound biosynthetic process0.95558.739e-09Moderately InformativeInherited
Biological Process (BP)reproduction0.016220.4624Moderately InformativeInherited
Biological Process (BP)DNA metabolic process01.425e-11InformativeDirect
Biological Process (BP)transcription, DNA-dependent0.0004480InformativeDirect
Biological Process (BP)response to DNA damage stimulus7.844e-071.907e-06InformativeDirect
Biological Process (BP)cellular macromolecular complex assembly00InformativeDirect
Biological Process (BP)chromosome organization00InformativeDirect
Biological Process (BP)protein complex assembly11InformativeInherited
Biological Process (BP)organelle assembly0.42430.274InformativeInherited
Biological Process (BP)protein localization to organelle0.065160.105InformativeInherited
Biological Process (BP)response to other organism0.1180.7305InformativeInherited
Biological Process (BP)defense response0.77840.6658InformativeInherited
Biological Process (BP)immune response0.32521InformativeInherited
Biological Process (BP)peptidyl-amino acid modification0.019190.002787InformativeInherited
Biological Process (BP)cell cycle process0.071620.06302InformativeInherited
Biological Process (BP)cellular process involved in reproduction1.146e-050.04252InformativeInherited
Biological Process (BP)transcription from RNA polymerase II promoter8.127e-081.162e-06Highly InformativeDirect
Biological Process (BP)internal protein amino acid acetylation8.2e-073.638e-12Highly InformativeDirect
Biological Process (BP)chromosome segregation4.679e-061.647e-12Highly InformativeDirect
Biological Process (BP)histone modification3.313e-051.45e-06Highly InformativeDirect
Biological Process (BP)peptidyl-lysine modification2.827e-059.574e-10Highly InformativeDirect
Biological Process (BP)chromatin assembly00Highly InformativeDirect
Biological Process (BP)defense response to bacterium4.255e-050.000158Highly InformativeDirect
Biological Process (BP)protein-DNA complex assembly00Highly InformativeDirect
Biological Process (BP)DNA replication0.0076530.2463Highly InformativeInherited
Biological Process (BP)humoral immune response0.0041750.01626Highly InformativeInherited
Biological Process (BP)innate immune response0.32060.5674Highly InformativeInherited
Biological Process (BP)meiosis0.0042260.006187Highly InformativeInherited
Biological Process (BP)DNA recombination0.99981Highly InformativeInherited
Molecular Function (MF)binding6.601e-111.237e-08Least InformativeDirect
Molecular Function (MF)nucleic acid binding00Moderately InformativeDirect
Molecular Function (MF)transferase activity, transferring phosphorus-containing groups0.90881Moderately InformativeInherited
Molecular Function (MF)nucleic acid binding transcription factor activity00InformativeDirect
Molecular Function (MF)DNA binding00InformativeDirect
Molecular Function (MF)chromatin binding9.806e-070.0001336InformativeDirect
Molecular Function (MF)nucleotidyltransferase activity0.020420.04691InformativeInherited
Molecular Function (MF)protein binding transcription factor activity0.00014995.819e-08Highly InformativeDirect
Molecular Function (MF)sequence-specific DNA binding transcription factor activity00Highly InformativeDirect
Molecular Function (MF)DNA polymerase activity1.74e-050.0001248Highly InformativeDirect
Molecular Function (MF)transcription regulatory region DNA binding2.687e-081.255e-07Highly InformativeDirect
Cellular Component (CC)intracellular non-membrane-bounded organelle4.009e-087.527e-05Least InformativeDirect
Cellular Component (CC)intracellular organelle part00Least InformativeDirect
Cellular Component (CC)protein complex11Least InformativeInherited
Cellular Component (CC)cytoplasmic part11Least InformativeInherited
Cellular Component (CC)intracellular membrane-bounded organelle0.075770.009963Least InformativeInherited
Cellular Component (CC)nuclear part00Moderately InformativeDirect
Cellular Component (CC)intracellular organelle lumen00Moderately InformativeDirect
Cellular Component (CC)vesicle11Moderately InformativeInherited
Cellular Component (CC)extracellular region part0.011690.1372Moderately InformativeInherited
Cellular Component (CC)chromosome00InformativeDirect
Cellular Component (CC)nucleoplasm part1.107e-050InformativeDirect
Cellular Component (CC)extracellular membrane-bounded organelle0.22610.1205InformativeInherited
Cellular Component (CC)nuclear DNA-directed RNA polymerase complex0.96652.975e-10InformativeInherited
Cellular Component (CC)chromatin6.341e-071.909e-05Highly InformativeDirect
Cellular Component (CC)transcription factor complex2.181e-050Highly InformativeDirect
Cellular Component (CC)lipid particle00Highly InformativeDirect
Cellular Component (CC)DNA polymerase complex3.835e-088.294e-12Highly InformativeDirect
Cellular Component (CC)nuclear chromosome part3.177e-080.0002544Highly InformativeDirect
Cellular Component (CC)SWI/SNF superfamily-type complex0.0013720.15Highly InformativeInherited
Cellular Component (CC)replisome0.010860.005077Highly InformativeInherited

Document: GO annotation of SCOP domains

Gene Ontology (high-coverage)

(show details)
GO term FDR (all) SDFO level Annotation (direct or inherited)
Biological Process (BP) cellular aromatic compound metabolic process 0 Least Informative Direct
Biological Process (BP) nitrogen compound metabolic process 9.966e-11 Least Informative Direct
Biological Process (BP) biosynthetic process 6.747e-05 Least Informative Direct
Biological Process (BP) regulation of metabolic process 0.0002179 Least Informative Direct
Biological Process (BP) cellular macromolecule metabolic process 4.219e-09 Least Informative Direct
Biological Process (BP) heterocycle metabolic process 0 Least Informative Direct
Biological Process (BP) cellular component organization or biogenesis 9.174e-10 Least Informative Direct
Biological Process (BP) organic cyclic compound metabolic process 1.611e-13 Least Informative Direct
Biological Process (BP) response to stimulus 1 Least Informative Inherited
Biological Process (BP) localization 1 Least Informative Inherited
Biological Process (BP) regulation of cellular process 0.7212 Least Informative Inherited
Biological Process (BP) protein metabolic process 1 Least Informative Inherited
Biological Process (BP) single-organism cellular process 0.1174 Least Informative Inherited
Biological Process (BP) organelle organization 0 Moderately Informative Direct
Biological Process (BP) regulation of biosynthetic process 1.325e-07 Moderately Informative Direct
Biological Process (BP) gene expression 5.895e-07 Moderately Informative Direct
Biological Process (BP) regulation of gene expression 2.531e-06 Moderately Informative Direct
Biological Process (BP) RNA metabolic process 1.372e-07 Moderately Informative Direct
Biological Process (BP) heterocycle biosynthetic process 1.494e-10 Moderately Informative Direct
Biological Process (BP) regulation of nucleobase-containing compound metabolic process 2.737e-12 Moderately Informative Direct
Biological Process (BP) aromatic compound biosynthetic process 9.596e-11 Moderately Informative Direct
Biological Process (BP) cellular macromolecule biosynthetic process 0 Moderately Informative Direct
Biological Process (BP) macromolecular complex subunit organization 1.354e-10 Moderately Informative Direct
Biological Process (BP) cellular component biogenesis 0.0005522 Moderately Informative Direct
Biological Process (BP) cellular nitrogen compound biosynthetic process 5.005e-11 Moderately Informative Direct
Biological Process (BP) organic cyclic compound biosynthetic process 8.739e-09 Moderately Informative Direct
Biological Process (BP) multi-organism process 0.2012 Moderately Informative Inherited
Biological Process (BP) macromolecule localization 1 Moderately Informative Inherited
Biological Process (BP) cellular localization 1 Moderately Informative Inherited
Biological Process (BP) cellular response to stress 0.03142 Moderately Informative Inherited
Biological Process (BP) cellular protein modification process 1 Moderately Informative Inherited
Biological Process (BP) immune system process 1 Moderately Informative Inherited
Biological Process (BP) reproduction 0.4624 Moderately Informative Inherited
Biological Process (BP) DNA metabolic process 1.425e-11 Informative Direct
Biological Process (BP) transcription, DNA-dependent 0 Informative Direct
Biological Process (BP) response to DNA damage stimulus 1.907e-06 Informative Direct
Biological Process (BP) cellular macromolecular complex assembly 0 Informative Direct
Biological Process (BP) chromosome organization 0 Informative Direct
Biological Process (BP) protein complex assembly 1 Informative Inherited
Biological Process (BP) organelle assembly 0.274 Informative Inherited
Biological Process (BP) protein localization to organelle 0.105 Informative Inherited
Biological Process (BP) response to other organism 0.7305 Informative Inherited
Biological Process (BP) defense response 0.6658 Informative Inherited
Biological Process (BP) immune response 1 Informative Inherited
Biological Process (BP) peptidyl-amino acid modification 0.002787 Informative Inherited
Biological Process (BP) cellular process involved in reproduction 0.04252 Informative Inherited
Biological Process (BP) cell cycle process 0.06302 Informative Inherited
Biological Process (BP) RNA processing 1 Informative Inherited
Biological Process (BP) mitotic cell cycle 0.3124 Informative Inherited
Biological Process (BP) transcription from RNA polymerase II promoter 1.162e-06 Highly Informative Direct
Biological Process (BP) internal protein amino acid acetylation 3.638e-12 Highly Informative Direct
Biological Process (BP) chromosome segregation 1.647e-12 Highly Informative Direct
Biological Process (BP) histone modification 1.45e-06 Highly Informative Direct
Biological Process (BP) peptidyl-lysine modification 9.574e-10 Highly Informative Direct
Biological Process (BP) chromatin assembly 0 Highly Informative Direct
Biological Process (BP) defense response to bacterium 0.000158 Highly Informative Direct
Biological Process (BP) protein-DNA complex assembly 0 Highly Informative Direct
Biological Process (BP) DNA replication 0.2463 Highly Informative Inherited
Biological Process (BP) humoral immune response 0.01626 Highly Informative Inherited
Biological Process (BP) symbiosis, encompassing mutualism through parasitism 0.05104 Highly Informative Inherited
Biological Process (BP) multi-organism cellular process 0.003531 Highly Informative Inherited
Biological Process (BP) innate immune response 0.5674 Highly Informative Inherited
Biological Process (BP) meiosis 0.006187 Highly Informative Inherited
Biological Process (BP) DNA recombination 1 Highly Informative Inherited
Biological Process (BP) RNA splicing 0.1046 Highly Informative Inherited
Biological Process (BP) mitosis 0.2563 Highly Informative Inherited
Molecular Function (MF) binding 1.237e-08 Least Informative Direct
Molecular Function (MF) nucleic acid binding 0 Moderately Informative Direct
Molecular Function (MF) transferase activity, transferring phosphorus-containing groups 1 Moderately Informative Inherited
Molecular Function (MF) enzyme regulator activity 0.5382 Moderately Informative Inherited
Molecular Function (MF) nucleic acid binding transcription factor activity 0 Informative Direct
Molecular Function (MF) DNA binding 0 Informative Direct
Molecular Function (MF) chromatin binding 0.0001336 Informative Direct
Molecular Function (MF) transferase activity, transferring acyl groups 0.1087 Informative Inherited
Molecular Function (MF) GTPase regulator activity 0.03828 Informative Inherited
Molecular Function (MF) nucleotidyltransferase activity 0.04691 Informative Inherited
Molecular Function (MF) protein binding transcription factor activity 5.819e-08 Highly Informative Direct
Molecular Function (MF) sequence-specific DNA binding transcription factor activity 0 Highly Informative Direct
Molecular Function (MF) guanyl-nucleotide exchange factor activity 0.0008749 Highly Informative Direct
Molecular Function (MF) transcription factor binding 3.656e-10 Highly Informative Direct
Molecular Function (MF) DNA polymerase activity 0.0001248 Highly Informative Direct
Molecular Function (MF) transcription regulatory region DNA binding 1.255e-07 Highly Informative Direct
Molecular Function (MF) acetyltransferase activity 0.002188 Highly Informative Inherited
Molecular Function (MF) small GTPase regulator activity 0.003813 Highly Informative Inherited
Cellular Component (CC) intracellular non-membrane-bounded organelle 7.527e-05 Least Informative Direct
Cellular Component (CC) intracellular organelle part 0 Least Informative Direct
Cellular Component (CC) protein complex 1 Least Informative Inherited
Cellular Component (CC) cytoplasmic part 1 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 0.009963 Least Informative Inherited
Cellular Component (CC) nuclear part 0 Moderately Informative Direct
Cellular Component (CC) intracellular organelle lumen 0 Moderately Informative Direct
Cellular Component (CC) vesicle 1 Moderately Informative Inherited
Cellular Component (CC) extracellular region part 0.1372 Moderately Informative Inherited
Cellular Component (CC) chromosome 0 Informative Direct
Cellular Component (CC) nucleoplasm part 0 Informative Direct
Cellular Component (CC) nuclear DNA-directed RNA polymerase complex 2.975e-10 Informative Direct
Cellular Component (CC) extracellular membrane-bounded organelle 0.1205 Informative Inherited
Cellular Component (CC) kinetochore 3.98e-05 Highly Informative Direct
Cellular Component (CC) chromatin 1.909e-05 Highly Informative Direct
Cellular Component (CC) transcription factor complex 0 Highly Informative Direct
Cellular Component (CC) lipid particle 0 Highly Informative Direct
Cellular Component (CC) DNA polymerase complex 8.294e-12 Highly Informative Direct
Cellular Component (CC) nuclear chromosome part 0.0002544 Highly Informative Direct
Cellular Component (CC) SWI/SNF superfamily-type complex 0.15 Highly Informative Inherited
Cellular Component (CC) replisome 0.005077 Highly Informative Inherited

Document: GO annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEO levelAnnotation (direct or inherited)
Enzyme Commission (EC)Nucleotidyltransferases0Least InformativeDirect
Enzyme Commission (EC)DNA-directed DNA polymerase0Moderately InformativeDirect

Document: EC annotation of SCOP domains

Mouse Phenotype (MP)

(show details)
MP termFDR (all)SDMP levelAnnotation (direct or inherited)
Mammalian Phenotype (MP)abnormal embryogenesis/ development1Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal preimplantation embryo development0.05591InformativeInherited
Mammalian Phenotype (MP)abnormal blastocyst morphology0.007478Highly InformativeInherited

Document: MP annotation of SCOP domains

Worm Phenotype (WP)

(show details)
WP termFDR (all)SDWP levelAnnotation (direct or inherited)
Worm Phenotype (WP)cell physiology variant0Least InformativeDirect
Worm Phenotype (WP)organism environmental stimulus response variant0.5346Least InformativeInherited
Worm Phenotype (WP)cell homeostasis metabolism variant0Moderately InformativeDirect
Worm Phenotype (WP)early embryonic lethal0Moderately InformativeDirect
Worm Phenotype (WP)locomotion variant3.072e-11Moderately InformativeDirect
Worm Phenotype (WP)gametogenesis variant5.892e-05Moderately InformativeDirect
Worm Phenotype (WP)reproductive system morphology variant0.0002031Moderately InformativeDirect
Worm Phenotype (WP)organ system development variant0.012Moderately InformativeInherited
Worm Phenotype (WP)organism segment morphology variant0.01602Moderately InformativeInherited
Worm Phenotype (WP)cell death variant0.4618Moderately InformativeInherited
Worm Phenotype (WP)cell division variant0InformativeDirect
Worm Phenotype (WP)chromosome segregation variant0InformativeDirect
Worm Phenotype (WP)meiotic chromosome organization variant7.995e-13InformativeDirect
Worm Phenotype (WP)alimentary system development variant2.643e-07InformativeDirect
Worm Phenotype (WP)protruding vulva3.745e-05InformativeDirect
Worm Phenotype (WP)cell corpse number variant0.005489InformativeInherited
Worm Phenotype (WP)organism pathogen response variant0.01066InformativeInherited
Worm Phenotype (WP)organism stress response variant0.08471InformativeInherited
Worm Phenotype (WP)body width variant0.2544InformativeInherited
Worm Phenotype (WP)diplotene progression during oogenesis variant0.2832InformativeInherited
Worm Phenotype (WP)body elongation variant0Highly InformativeDirect
Worm Phenotype (WP)pharyngeal development variant1.717e-14Highly InformativeDirect
Worm Phenotype (WP)embryonic arrest2.499e-13Highly InformativeDirect
Worm Phenotype (WP)stress induced lethality increased1.048e-07Highly InformativeDirect
Worm Phenotype (WP)organism osmotic stress response variant2.574e-06Highly InformativeDirect
Worm Phenotype (WP)chromosome condensation variant1.192e-05Highly InformativeDirect
Worm Phenotype (WP)pathogen susceptibility increased6.252e-05Highly InformativeDirect

Document: WP annotation of SCOP domains

Yeast Phenotype (YP)

(show details)
YP termFDR (all)SDYP levelAnnotation (direct or inherited)
Yeast Phenotype (YP)cell cycle progression0.002121InformativeInherited
Yeast Phenotype (YP)cell cycle progression in G2 phase8.664e-05Highly InformativeDirect
Yeast Phenotype (YP)budding0.0002859Highly InformativeDirect

Document: YP annotation of SCOP domains

Fly Anatomy (FA)

(show details) Document: FA annotation of SCOP domains

Xenopus Anatomy (XA)

(show details)
XA termFDR (all)SDXA levelAnnotation (direct or inherited)
Xenopus ANatomical entity (XAN)genital system0Least InformativeDirect

Document: XA annotation of SCOP domains

Arabidopsis Plant Ontology (AP)

(show details)
AP termFDR (all)SDAP levelAnnotation (direct or inherited)
Plant ANatomical entity (PAN)root system0.2379Least InformativeInherited
Plant ANatomical entity (PAN)portion of meristem tissue0.7048Least InformativeInherited
Plant ANatomical entity (PAN)cardinal part of multi-tissue plant structure0.8912Least InformativeInherited
Plant ANatomical entity (PAN)shoot axis0.9364Least InformativeInherited
Plant ANatomical entity (PAN)primordium0.0008924InformativeDirect
Plant ANatomical entity (PAN)root tip0.01274InformativeInherited
Plant ANatomical entity (PAN)lateral root primordium6.482e-06Highly InformativeDirect
Plant ANatomical entity (PAN)lateral root1.515e-05Highly InformativeDirect
Plant ANatomical entity (PAN)reproductive shoot apex7.867e-05Highly InformativeDirect
Plant ANatomical entity (PAN)root meristem0.0001122Highly InformativeDirect
Plant ANatomical entity (PAN)shoot apical meristem0.000585Highly InformativeDirect
Plant structure DEvelopment stage (PDE)seedling development stage2.424e-07InformativeDirect

Document: AP annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEC levelAnnotation (direct or inherited)
Enzyme Commission (EC)Transferring phosphorous-containing groups0Least InformativeDirect
Enzyme Commission (EC)Nucleotidyltransferases0Moderately InformativeDirect
Enzyme Commission (EC)DNA-directed DNA polymerase0InformativeDirect

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processTranscription regulation8.681e-12Moderately InformativeDirect
Biological processDNA damage1.964e-05Moderately InformativeDirect
Biological processCell cycle0.4067Moderately InformativeInherited
Biological processMitosis5.296e-08InformativeDirect
Cellular componentNucleus0Least InformativeDirect
Cellular componentChromosome0InformativeDirect
Cellular componentCentromere0Highly InformativeDirect
Cellular componentKinetochore0Highly InformativeDirect
Molecular functionDNA-binding0Moderately InformativeDirect
Post-translational modificationTransferase1Least InformativeInherited
Post-translational modificationActivator0Moderately InformativeDirect
Post-translational modificationNucleotidyltransferase0.4827Moderately InformativeInherited
Post-translational modificationDNA-directed DNA polymerase0InformativeDirect
Post-translational modificationAntimicrobial3.895e-10InformativeDirect
Post-translational modificationChromatin regulator2.558e-09InformativeDirect
Post-translational modificationGuanine-nucleotide releasing factor0.0007099InformativeDirect
Post-translational modificationAntibiotic2.368e-13Highly InformativeDirect
Post-translational modificationAcetylation0Least InformativeDirect
Post-translational modificationPhosphoprotein0Least InformativeDirect
Post-translational modificationMethylation0Moderately InformativeDirect
Post-translational modificationUbl conjugation0Moderately InformativeDirect
Post-translational modificationIsopeptide bond0Moderately InformativeDirect
Post-translational modificationCitrullination0Highly InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR009072 SSF47113 Protein matches
Abstract

Histones mediate DNA organisation and plays a dominant role in regulating eukaryotic transcription. The histone-fold consists of a core of three helices, where the long middle helix is flanked at each end by shorter ones. Proteins displaying this structure include the nucleosome core histones, which form octomers composed of two copies of each of the four histones, H2A, H2B, H3 and H4; archaeal histone, which possesses only the core domain part of eukaryotic histone; and the TATA-box binding protein (TBP)-associated factors (TAF), where the histone fold is a common motif for mediating TAF-TAF interactions. TAF proteins include TAF(II)18 and TAF(II)28, which form a heterodimer, TAF(II)42 and TAF(II)62, which form a heterotetramer similar to (H3-H4)2, and the negative cofactor 2 (NC2) alpha and beta chains, which form a heterodimer. The TAF proteins are a component of transcription factor IID (TFIID), along with the TBP protein. TFIID forms part of the pre-initiation complex on core promoter elements required for RNA polymerase II-dependent transcription. The TAF subunits of TFIID mediate transcriptional activation of subsets of eukaryotic genes. The NC2 complex mediates the inhibition of TATA-dependent transcription through interactions with TBP.


InterPro database


PDBeMotif information about ligands, sequence and structure motifs
Cross references PDB entries
Ligand binding statistics
Nucleic-acid binding statistics
Occurrence of secondary structure elements
Occurrence of small 3D structural motifs

PDBeMotif resource

Jump to [ Top of page · SCOP classification · InterPro annotation · PDBeMotif links · Functional annotation · Gene Ontology (high-quality) · Gene Ontology (high-coverage) · Enzyme Commission (EC) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Fly Anatomy (FA) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) ]

Internal database links

Browse genome assignments for this superfamily. The SUPERFAMILY hidden Markov model library has been used to carry out SCOP domain assignments to all genomes at the superfamily level.


Alignments of sequences to 32 models in this superfamily are available by clicking on the 'Alignments' icon above. PDB sequences less than 40% identical are shown by default, but any other sequence(s) may be aligned. Select PDB sequences, genome sequences, or paste in or upload your own sequences.


Browse and view proteins in genomes which have different domain combinations including a Histone-fold domain.


Examine the distribution of domain superfamilies, or families, across the major taxonomic kingdoms or genomes within a kingdom. This gives an immediate impression of how superfamilies, or families, are restricted to certain kingdoms of life.


Explore domain occurrence network where nodes represent genomes and edges are domain architectures (shared between genomes) containing the superfamily of interest.

There are 32 hidden Markov models representing the Histone-fold superfamily. Information on how the models are built, and plots showing hydrophobicity, match emmission probabilities and insertion/deletion probabilities can be inspected.


Jump to [ Top of page · SCOP classification · InterPro annotation · PDBeMotif links · Functional annotation · Gene Ontology (high-quality) · Gene Ontology (high-coverage) · Enzyme Commission (EC) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Fly Anatomy (FA) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · Internal database links ]