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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 (664) Uniprot 2018_03 genome PDB chains (SCOP 1.75)
Domains 28,154 87,784 82
Proteins 27,725 86,141 81


Functional annotation
General category Regulation
Detailed category DNA-binding

Document:
Function annotation of SCOP domain superfamilies

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

Human Phenotype (HP)

(show details)
HP termFDR (all)SDHP levelAnnotation (direct or inherited)
Phenotypic Abnormality (PA)Abnormality of skeletal morphology0.1226Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of limbs0.1396Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the head0.146Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the integument0.2381Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of skin adnexa morphology0.03128Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of limb bone morphology0.0498Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of skeletal physiology0.0947Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormal joint morphology0.1822Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the upper limb0.4155Moderately InformativeInherited
Phenotypic Abnormality (PA)Congenital abnormal hair pattern0.0006453InformativeDirect
Phenotypic Abnormality (PA)Abnormality of the ulna0.0003741Highly InformativeDirect
Phenotypic Abnormality (PA)Synostosis of joints0.0006985Highly InformativeDirect
Phenotypic Abnormality (PA)Abnormality of the radius0.0009478Highly InformativeDirect

Document: HP annotation of SCOP domains

Mouse Phenotype (MP)

(show details)
MP termFDR (all)SDMP levelAnnotation (direct or inherited)
Mammalian Phenotype (MP)embryo phenotype0.1613Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal preimplantation embryo morphology0.02035Highly 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 variant8.918e-16Least InformativeDirect
Worm Phenotype (WP)blast cell physiology variant8.918e-16Least InformativeDirect
Worm Phenotype (WP)cell morphology variant0.0000000000002974Least InformativeDirect
Worm Phenotype (WP)organism metabolism processing variant0.00000000097Least InformativeDirect
Worm Phenotype (WP)organism behavior variant0.000000009859Least InformativeDirect
Worm Phenotype (WP)organism environmental stimulus response variant0.0001883Least InformativeDirect
Worm Phenotype (WP)organ system morphology variant0.00215Least InformativeInherited
Worm Phenotype (WP)cell development variant0.07915Least InformativeInherited
Worm Phenotype (WP)cell homeostasis metabolism variant0Moderately InformativeDirect
Worm Phenotype (WP)cell division variant0Moderately InformativeDirect
Worm Phenotype (WP)early embryonic lethal0Moderately InformativeDirect
Worm Phenotype (WP)apoptosis variant0.000007371Moderately InformativeDirect
Worm Phenotype (WP)feeding behavior variant0.000009017Moderately InformativeDirect
Worm Phenotype (WP)germ cell development variant0.0002357Moderately InformativeDirect
Worm Phenotype (WP)reproductive system morphology variant0.03472Moderately InformativeInherited
Worm Phenotype (WP)body region morphology variant0.2128Moderately InformativeInherited
Worm Phenotype (WP)organism segment morphology variant0.2128Moderately InformativeInherited
Worm Phenotype (WP)developmental morphology variant0.2136Moderately InformativeInherited
Worm Phenotype (WP)adult body morphology variant0.2144Moderately InformativeInherited
Worm Phenotype (WP)body morphology variant0.2355Moderately InformativeInherited
Worm Phenotype (WP)organism stress response variant1Moderately InformativeInherited
Worm Phenotype (WP)germ cell differentiation variant1Moderately InformativeInherited
Worm Phenotype (WP)chromosome segregation variant0InformativeDirect
Worm Phenotype (WP)cytokinesis variant emb0InformativeDirect
Worm Phenotype (WP)vesicle morphology variant0InformativeDirect
Worm Phenotype (WP)cell component localization variant0InformativeDirect
Worm Phenotype (WP)avoids bacterial lawn4.465e-16InformativeDirect
Worm Phenotype (WP)meiotic chromosome organization variant0.000000000001155InformativeDirect
Worm Phenotype (WP)life span variant0.00000000004996InformativeDirect
Worm Phenotype (WP)organism pathogen response variant0.00000001586InformativeDirect
Worm Phenotype (WP)alimentary system development variant0.00000154InformativeDirect
Worm Phenotype (WP)protruding vulva0.00000949InformativeDirect
Worm Phenotype (WP)mitosis variant0.02447InformativeInherited
Worm Phenotype (WP)diplotene progression during oogenesis variant0.2471InformativeInherited
Worm Phenotype (WP)cytokinesis defective early emb0Highly InformativeDirect
Worm Phenotype (WP)body elongation variant0Highly InformativeDirect
Worm Phenotype (WP)lysosome-related organelle morphology variant0Highly InformativeDirect
Worm Phenotype (WP)RAB-11 recycling endosome localization variant0Highly InformativeDirect
Worm Phenotype (WP)no induction of antimicrobial peptide expression after infection0Highly InformativeDirect
Worm Phenotype (WP)pharyngeal development variant0.00000000000003016Highly InformativeDirect
Worm Phenotype (WP)embryonic arrest0.00000000001749Highly InformativeDirect
Worm Phenotype (WP)dauer arrest variant0.0000000629Highly InformativeDirect
Worm Phenotype (WP)chromosome condensation variant0.000001348Highly InformativeDirect
Worm Phenotype (WP)organism osmotic stress response variant0.000009832Highly InformativeDirect
Worm Phenotype (WP)alimentary system morphology variant0.06505Highly InformativeInherited

Document: WP annotation of SCOP domains

Yeast Phenotype (YP)

(show details)
YP termFDR (all)SDYP levelAnnotation (direct or inherited)
Yeast Phenotype (YP)cell cycle progression0.002305InformativeInherited
Yeast Phenotype (YP)cell cycle progression in G2 phase0.00008639Highly InformativeDirect
Yeast Phenotype (YP)budding0.0002206Highly InformativeDirect

Document: YP annotation of SCOP domains

Fly Anatomy (FA)

(show details)
FA termFDR (all)SDFA levelAnnotation (direct or inherited)
Fly Anatomy (FA)larva0.2328Least InformativeInherited
Fly Anatomy (FA)embryo0.4596Moderately InformativeInherited
Fly Anatomy (FA)fat body0.001972InformativeInherited
Fly Anatomy (FA)embryonic/larval fat body0.0004912Highly InformativeDirect

Document: FA annotation of SCOP domains

Zebrafish Anatomy (ZA)

(show details) Document: ZA annotation of SCOP domains

Xenopus Anatomy (XA)

(show details) 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 system0.2392Least InformativeInherited
Plant ANatomical entity (PAN)portion of meristem tissue0.7063Least InformativeInherited
Plant ANatomical entity (PAN)cardinal part of multi-tissue plant structure0.8923Least InformativeInherited
Plant ANatomical entity (PAN)shoot axis0.937Least InformativeInherited
Plant ANatomical entity (PAN)primordium0.0008976InformativeDirect
Plant ANatomical entity (PAN)root tip0.01302InformativeInherited
Plant ANatomical entity (PAN)lateral root primordium0.000006522Highly InformativeDirect
Plant ANatomical entity (PAN)lateral root0.00001524Highly InformativeDirect
Plant ANatomical entity (PAN)reproductive shoot apex0.00007921Highly InformativeDirect
Plant ANatomical entity (PAN)root meristem0.0001129Highly InformativeDirect
Plant ANatomical entity (PAN)shoot apical meristem0.0005886Highly InformativeDirect
Plant structure DEvelopment stage (PDE)seedling development stage0.0000002535InformativeDirect

Document: AP 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 · Enzyme Commission (EC) · Human Phenotype (HP) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Fly Anatomy (FA) · Zebrafish Anatomy (ZA) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) ]

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 46 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 46 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 · Enzyme Commission (EC) · Human Phenotype (HP) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Fly Anatomy (FA) · Zebrafish Anatomy (ZA) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · Internal database links ]