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 (656) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 27,778 39,243 82
Proteins 27,341 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 process0.0000000010360Least InformativeDirect
Biological Process (BP)nitrogen compound metabolic process0.0000032530.000000000001107Least InformativeDirect
Biological Process (BP)cellular macromolecule metabolic process0.0000000026810.00000000004732Least InformativeDirect
Biological Process (BP)heterocycle metabolic process0.00000000084410Least InformativeDirect
Biological Process (BP)cellular component organization or biogenesis00.0000000000008048Least InformativeDirect
Biological Process (BP)organic cyclic compound metabolic process0.000000030980Least InformativeDirect
Biological Process (BP)regulation of cellular process0.89330.3667Least InformativeInherited
Biological Process (BP)regulation of metabolic process0.14950.00005299Least InformativeInherited
Biological Process (BP)localization11Least InformativeInherited
Biological Process (BP)protein metabolic process11Least InformativeInherited
Biological Process (BP)biosynthetic process0.84370.000005522Least InformativeInherited
Biological Process (BP)single-organism metabolic process11Least InformativeInherited
Biological Process (BP)response to stimulus0.098821Least InformativeInherited
Biological Process (BP)single-organism cellular process11Least InformativeInherited
Biological Process (BP)regulation of macromolecule biosynthetic process0.0000089240.000000000487Moderately InformativeDirect
Biological Process (BP)regulation of nucleobase-containing compound metabolic process0.000093060.00000000000005988Moderately InformativeDirect
Biological Process (BP)regulation of cellular biosynthetic process0.000037230.000001066Moderately InformativeDirect
Biological Process (BP)macromolecular complex subunit organization0.0000000000045250Moderately InformativeDirect
Biological Process (BP)single-organism organelle organization0.000089440.0007552Moderately InformativeDirect
Biological Process (BP)regulation of gene expression0.03990.000008276Moderately InformativeInherited
Biological Process (BP)negative regulation of metabolic process0.30980.3914Moderately InformativeInherited
Biological Process (BP)response to external stimulus0.41231Moderately InformativeInherited
Biological Process (BP)multi-organism process0.0034030.1402Moderately InformativeInherited
Biological Process (BP)cellular component biogenesis0.04930.001038Moderately InformativeInherited
Biological Process (BP)macromolecule localization0.7891Moderately InformativeInherited
Biological Process (BP)cellular localization0.98621Moderately InformativeInherited
Biological Process (BP)cellular nitrogen compound biosynthetic process0.34560.0000000000006548Moderately InformativeInherited
Biological Process (BP)cellular response to stress0.00012890.007607Moderately InformativeInherited
Biological Process (BP)cellular protein modification process0.52161Moderately InformativeInherited
Biological Process (BP)RNA metabolic process0.77910.000000006125Moderately InformativeInherited
Biological Process (BP)aromatic compound biosynthetic process0.23970.000000000001329Moderately InformativeInherited
Biological Process (BP)heterocycle biosynthetic process0.4080.000000000002225Moderately InformativeInherited
Biological Process (BP)cellular macromolecule biosynthetic process0.0043950Moderately InformativeInherited
Biological Process (BP)organic cyclic compound biosynthetic process0.52340.0000000001906Moderately InformativeInherited
Biological Process (BP)gene expression0.86710.0000006489Moderately InformativeInherited
Biological Process (BP)immune system process0.41051Moderately InformativeInherited
Biological Process (BP)defense response0.80750.6655Moderately InformativeInherited
Biological Process (BP)DNA repair0.0000049070.0005524InformativeDirect
Biological Process (BP)transcription, DNA-templated0.000081110InformativeDirect
Biological Process (BP)cellular macromolecular complex assembly00.000000000003345InformativeDirect
Biological Process (BP)chromosome organization00InformativeDirect
Biological Process (BP)organelle assembly0.61350.4661InformativeInherited
Biological Process (BP)cell cycle process0.0031870.003486InformativeInherited
Biological Process (BP)organelle fission0.58420.6246InformativeInherited
Biological Process (BP)defense response to other organism0.002080.0158InformativeInherited
Biological Process (BP)protein localization to organelle0.062140.08916InformativeInherited
Biological Process (BP)response to bacterium0.00011990.008968InformativeInherited
Biological Process (BP)immune response0.33010.9915InformativeInherited
Biological Process (BP)peptidyl-amino acid modification0.013990.001979InformativeInherited
Biological Process (BP)cell division0.0057660.01052InformativeInherited
Biological Process (BP)nuclear division0.00015720.0000655Highly InformativeDirect
Biological Process (BP)internal protein amino acid acetylation0.0000010880.00000000000211Highly InformativeDirect
Biological Process (BP)chromosome segregation0.000000075110.0000000000002301Highly InformativeDirect
Biological Process (BP)histone modification0.00002550.0000008432Highly InformativeDirect
Biological Process (BP)peptidyl-lysine modification0.00002970.0000000006117Highly InformativeDirect
Biological Process (BP)defense response to bacterium0.00041790.0001357Highly InformativeDirect
Biological Process (BP)regulation of gene expression, epigenetic0.063110.1771Highly InformativeInherited
Biological Process (BP)DNA replication0.045610.4335Highly InformativeInherited
Biological Process (BP)humoral immune response0.0036050.01294Highly InformativeInherited
Biological Process (BP)meiotic cell cycle0.00031080.03108Highly InformativeInherited
Biological Process (BP)transcription from RNA polymerase II promoter0.0067750.00002222Highly InformativeInherited
Biological Process (BP)innate immune response0.30920.5352Highly InformativeInherited
Biological Process (BP)DNA recombination11Highly InformativeInherited
Molecular Function (MF)binding0.000000000033660.0000000005292Least InformativeDirect
Molecular Function (MF)transferase activity11Least InformativeInherited
Molecular Function (MF)nucleic acid binding00Moderately InformativeDirect
Molecular Function (MF)transferase activity, transferring phosphorus-containing groups0.90121Moderately InformativeInherited
Molecular Function (MF)nucleic acid binding transcription factor activity00InformativeDirect
Molecular Function (MF)DNA binding00InformativeDirect
Molecular Function (MF)chromatin binding0.0000010360.0001644InformativeDirect
Molecular Function (MF)nucleotidyltransferase activity0.019790.04064InformativeInherited
Molecular Function (MF)transcription factor binding transcription factor activity0.00012110.00000001398Highly InformativeDirect
Molecular Function (MF)DNA polymerase activity0.000015350.00009852Highly InformativeDirect
Molecular Function (MF)transcription regulatory region DNA binding0.000000068690.0000002251Highly InformativeDirect
Cellular Component (CC)non-membrane-bounded organelle00.000000000358Least InformativeDirect
Cellular Component (CC)intracellular organelle part00Least InformativeDirect
Cellular Component (CC)intracellular membrane-bounded organelle0.015420.000342Least InformativeInherited
Cellular Component (CC)protein complex0.0020120.000004476Least InformativeInherited
Cellular Component (CC)nuclear part00Moderately InformativeDirect
Cellular Component (CC)intracellular organelle lumen00Moderately InformativeDirect
Cellular Component (CC)transferase complex00Moderately InformativeDirect
Cellular Component (CC)extracellular region part0.00093770.005834Moderately InformativeInherited
Cellular Component (CC)vesicle11Moderately InformativeInherited
Cellular Component (CC)DNA-directed RNA polymerase complex0.000065650InformativeDirect
Cellular Component (CC)chromosome00InformativeDirect
Cellular Component (CC)lipid particle0.000000000056070.000000000004964InformativeDirect
Cellular Component (CC)nucleoplasm part0.0000030650.000000000000006018InformativeDirect
Cellular Component (CC)extracellular membrane-bounded organelle0.11910.02754InformativeInherited
Cellular Component (CC)chromosome, centromeric region0.00000000000062370.0001222Highly InformativeDirect
Cellular Component (CC)chromatin00Highly InformativeDirect
Cellular Component (CC)protein acetyltransferase complex00Highly InformativeDirect
Cellular Component (CC)DNA polymerase complex0.000000043630.00000000001112Highly InformativeDirect
Cellular Component (CC)nuclear chromosome part0.000000012730.0005109Highly InformativeDirect

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 0.000000000001107 Least Informative Direct
Biological Process (BP) biosynthetic process 0.000005522 Least Informative Direct
Biological Process (BP) regulation of metabolic process 0.00005299 Least Informative Direct
Biological Process (BP) cellular macromolecule metabolic process 0.00000000004732 Least Informative Direct
Biological Process (BP) heterocycle metabolic process 0 Least Informative Direct
Biological Process (BP) cellular component organization or biogenesis 0.0000000000008048 Least Informative Direct
Biological Process (BP) organic cyclic compound metabolic process 0 Least Informative Direct
Biological Process (BP) localization 1 Least Informative Inherited
Biological Process (BP) regulation of cellular process 0.3667 Least Informative Inherited
Biological Process (BP) protein metabolic process 1 Least Informative Inherited
Biological Process (BP) single-organism metabolic process 1 Least Informative Inherited
Biological Process (BP) response to stimulus 1 Least Informative Inherited
Biological Process (BP) single-organism cellular process 1 Least Informative Inherited
Biological Process (BP) gene expression 0.0000006489 Moderately Informative Direct
Biological Process (BP) regulation of gene expression 0.000008276 Moderately Informative Direct
Biological Process (BP) regulation of macromolecule biosynthetic process 0.000000000487 Moderately Informative Direct
Biological Process (BP) RNA metabolic process 0.000000006125 Moderately Informative Direct
Biological Process (BP) heterocycle biosynthetic process 0.000000000002225 Moderately Informative Direct
Biological Process (BP) regulation of nucleobase-containing compound metabolic process 0.00000000000005988 Moderately Informative Direct
Biological Process (BP) aromatic compound biosynthetic process 0.000000000001329 Moderately Informative Direct
Biological Process (BP) regulation of cellular biosynthetic process 0.000001066 Moderately Informative Direct
Biological Process (BP) cellular macromolecule biosynthetic process 0 Moderately Informative Direct
Biological Process (BP) macromolecular complex subunit organization 0 Moderately Informative Direct
Biological Process (BP) cellular nitrogen compound biosynthetic process 0.0000000000006548 Moderately Informative Direct
Biological Process (BP) organic cyclic compound biosynthetic process 0.0000000001906 Moderately Informative Direct
Biological Process (BP) single-organism organelle organization 0.0007552 Moderately Informative Direct
Biological Process (BP) negative regulation of metabolic process 0.3914 Moderately Informative Inherited
Biological Process (BP) multi-organism process 0.1402 Moderately Informative Inherited
Biological Process (BP) response to external stimulus 1 Moderately Informative Inherited
Biological Process (BP) cellular component biogenesis 0.001038 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 0.007607 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) defense response 0.6655 Moderately Informative Inherited
Biological Process (BP) DNA repair 0.0005524 Informative Direct
Biological Process (BP) transcription, DNA-templated 0 Informative Direct
Biological Process (BP) cellular macromolecular complex assembly 0.000000000003345 Informative Direct
Biological Process (BP) chromosome organization 0 Informative Direct
Biological Process (BP) organelle assembly 0.4661 Informative Inherited
Biological Process (BP) cell cycle process 0.003486 Informative Inherited
Biological Process (BP) organelle fission 0.6246 Informative Inherited
Biological Process (BP) defense response to other organism 0.0158 Informative Inherited
Biological Process (BP) protein localization to organelle 0.08916 Informative Inherited
Biological Process (BP) response to bacterium 0.008968 Informative Inherited
Biological Process (BP) immune response 0.9915 Informative Inherited
Biological Process (BP) peptidyl-amino acid modification 0.001979 Informative Inherited
Biological Process (BP) RNA processing 1 Informative Inherited
Biological Process (BP) cell division 0.01052 Informative Inherited
Biological Process (BP) mitotic cell cycle 0.3136 Informative Inherited
Biological Process (BP) nuclear division 0.0000655 Highly Informative Direct
Biological Process (BP) transcription from RNA polymerase II promoter 0.00002222 Highly Informative Direct
Biological Process (BP) internal protein amino acid acetylation 0.00000000000211 Highly Informative Direct
Biological Process (BP) chromosome segregation 0.0000000000002301 Highly Informative Direct
Biological Process (BP) histone modification 0.0000008432 Highly Informative Direct
Biological Process (BP) peptidyl-lysine modification 0.0000000006117 Highly Informative Direct
Biological Process (BP) defense response to bacterium 0.0001357 Highly Informative Direct
Biological Process (BP) regulation of gene expression, epigenetic 0.1771 Highly Informative Inherited
Biological Process (BP) DNA replication 0.4335 Highly Informative Inherited
Biological Process (BP) humoral immune response 0.01294 Highly Informative Inherited
Biological Process (BP) symbiosis, encompassing mutualism through parasitism 0.06776 Highly Informative Inherited
Biological Process (BP) multi-organism cellular process 0.004412 Highly Informative Inherited
Biological Process (BP) meiotic cell cycle 0.03108 Highly Informative Inherited
Biological Process (BP) innate immune response 0.5352 Highly Informative Inherited
Biological Process (BP) DNA recombination 1 Highly Informative Inherited
Biological Process (BP) RNA splicing 0.09124 Highly Informative Inherited
Molecular Function (MF) binding 0.0000000005292 Least Informative Direct
Molecular Function (MF) transferase activity 1 Least Informative Inherited
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) nucleic acid binding transcription factor activity 0 Informative Direct
Molecular Function (MF) DNA binding 0 Informative Direct
Molecular Function (MF) chromatin binding 0.0001644 Informative Direct
Molecular Function (MF) nucleotidyltransferase activity 0.04064 Informative Inherited
Molecular Function (MF) transferase activity, transferring acyl groups 0.1011 Informative Inherited
Molecular Function (MF) transcription factor binding transcription factor activity 0.00000001398 Highly Informative Direct
Molecular Function (MF) guanyl-nucleotide exchange factor activity 0.0006577 Highly Informative Direct
Molecular Function (MF) transcription factor binding 0.000000000445 Highly Informative Direct
Molecular Function (MF) DNA polymerase activity 0.00009852 Highly Informative Direct
Molecular Function (MF) transcription regulatory region DNA binding 0.0000002251 Highly Informative Direct
Molecular Function (MF) acetyltransferase activity 0.001863 Highly Informative Inherited
Cellular Component (CC) non-membrane-bounded organelle 0.000000000358 Least Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 0.000342 Least Informative Direct
Cellular Component (CC) protein complex 0.000004476 Least Informative Direct
Cellular Component (CC) intracellular organelle part 0 Least Informative Direct
Cellular Component (CC) nuclear part 0 Moderately Informative Direct
Cellular Component (CC) intracellular organelle lumen 0 Moderately Informative Direct
Cellular Component (CC) transferase complex 0 Moderately Informative Direct
Cellular Component (CC) extracellular region part 0.005834 Moderately Informative Inherited
Cellular Component (CC) vesicle 1 Moderately Informative Inherited
Cellular Component (CC) DNA-directed RNA polymerase complex 0 Informative Direct
Cellular Component (CC) chromosome 0 Informative Direct
Cellular Component (CC) lipid particle 0.000000000004964 Informative Direct
Cellular Component (CC) nucleoplasm part 0.000000000000006018 Informative Direct
Cellular Component (CC) extracellular membrane-bounded organelle 0.02754 Informative Inherited
Cellular Component (CC) chromosome, centromeric region 0.0001222 Highly Informative Direct
Cellular Component (CC) chromatin 0 Highly Informative Direct
Cellular Component (CC) protein acetyltransferase complex 0 Highly Informative Direct
Cellular Component (CC) DNA polymerase complex 0.00000000001112 Highly Informative Direct
Cellular Component (CC) nuclear chromosome part 0.0005109 Highly Informative Direct

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 blastocyst morphology0.007799Highly 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 variant0.00000000003072Moderately InformativeDirect
Worm Phenotype (WP)gametogenesis variant0.00005892Moderately 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 variant0.0000000000007995InformativeDirect
Worm Phenotype (WP)alimentary system development variant0.0000002643InformativeDirect
Worm Phenotype (WP)protruding vulva0.00003745InformativeDirect
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 variant0.00000000000001717Highly InformativeDirect
Worm Phenotype (WP)embryonic arrest0.0000000000002499Highly InformativeDirect
Worm Phenotype (WP)stress induced lethality increased0.0000001048Highly InformativeDirect
Worm Phenotype (WP)organism osmotic stress response variant0.000002574Highly InformativeDirect
Worm Phenotype (WP)chromosome condensation variant0.00001192Highly InformativeDirect
Worm Phenotype (WP)pathogen susceptibility increased0.00006252Highly 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 progression0.002133InformativeInherited
Yeast Phenotype (YP)cell cycle progression in G2 phase0.00008735Highly InformativeDirect
Yeast Phenotype (YP)budding0.0002806Highly 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 primordium0.000006482Highly InformativeDirect
Plant ANatomical entity (PAN)lateral root0.00001515Highly InformativeDirect
Plant ANatomical entity (PAN)reproductive shoot apex0.00007867Highly 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 stage0.0000002424InformativeDirect

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 regulation0.000000000009598Moderately InformativeDirect
Biological processDNA damage0.00001922Moderately InformativeDirect
Biological processCell cycle0.3847Moderately InformativeInherited
Biological processMitosis0.00000004209InformativeDirect
Cellular componentNucleus0Least InformativeDirect
Cellular componentChromosome0InformativeDirect
Cellular componentCentromere0Highly InformativeDirect
Cellular componentKinetochore0Highly InformativeDirect
Molecular functionDNA-binding0Least InformativeDirect
Post-translational modificationTransferase1Least InformativeInherited
Post-translational modificationActivator0Moderately InformativeDirect
Post-translational modificationNucleotidyltransferase0.4789Moderately InformativeInherited
Post-translational modificationDNA-directed DNA polymerase0InformativeDirect
Post-translational modificationAntimicrobial0.0000000003757InformativeDirect
Post-translational modificationChromatin regulator0.000000002834InformativeDirect
Post-translational modificationGuanine-nucleotide releasing factor0.0007016InformativeDirect
Post-translational modificationAntibiotic0.0000000000002275Highly 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 ]