SUPERFAMILY 1.75 HMM library and genome assignments server


ENTH/VHS domain superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   All alpha proteins [ 46456] (284)
Fold:   alpha-alpha superhelix [ 48370] (24)
Superfamily:   ENTH/VHS domain [ 48464] (4)
Families:   ENTH domain [ 48465]
  VHS domain [ 48468] (5)
  Phosphoinositide-binding clathrin adaptor, N-terminal domain [ 100911] (2)
  RPR domain (SMART 00582 ) [ 109975]


Superfamily statistics
Genomes (497) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 9,688 9,644 14
Proteins 9,655 9,623 14


Functional annotation
General category Processes_IC
Detailed category Transport

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)developmental process0.00073791Least InformativeInherited
Biological Process (BP)multicellular organismal process0.0015490.9708Least InformativeInherited
Biological Process (BP)single-organism cellular process0.01450.00878Least InformativeInherited
Biological Process (BP)response to stimulus0.055941Least InformativeInherited
Biological Process (BP)regulation of cellular process0.67240.8631Least InformativeInherited
Biological Process (BP)organ development0.14221Moderately InformativeInherited
Biological Process (BP)signal transduction0.00074040.2296Moderately InformativeInherited
Biological Process (BP)embryonic organ development1.035e-070.000444InformativeDirect
Biological Process (BP)embryo development ending in birth or egg hatching9.349e-070.01696InformativeInherited

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) localization 3.755e-15 Least Informative Direct
Biological Process (BP) regulation of cellular process 0.8631 Least Informative Inherited
Biological Process (BP) developmental process 1 Least Informative Inherited
Biological Process (BP) regulation of metabolic process 1 Least Informative Inherited
Biological Process (BP) protein metabolic process 1 Least Informative Inherited
Biological Process (BP) single-organism cellular process 0.00878 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 0.54 Least Informative Inherited
Biological Process (BP) multicellular organismal process 0.9708 Least Informative Inherited
Biological Process (BP) response to stimulus 1 Least Informative Inherited
Biological Process (BP) cellular macromolecule metabolic process 1 Least Informative Inherited
Biological Process (BP) cellular aromatic compound metabolic process 1 Least Informative Inherited
Biological Process (BP) heterocycle metabolic process 1 Least Informative Inherited
Biological Process (BP) organic cyclic compound metabolic process 1 Least Informative Inherited
Biological Process (BP) nitrogen compound metabolic process 1 Least Informative Inherited
Biological Process (BP) cellular localization 0 Moderately Informative Direct
Biological Process (BP) system process 0.0004696 Moderately Informative Direct
Biological Process (BP) regulation of developmental process 0.3914 Moderately Informative Inherited
Biological Process (BP) negative regulation of cellular process 0.5343 Moderately Informative Inherited
Biological Process (BP) macromolecular complex subunit organization 0.001945 Moderately Informative Inherited
Biological Process (BP) regulation of macromolecule biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) regulation of nucleobase-containing compound metabolic process 1 Moderately Informative Inherited
Biological Process (BP) phosphate-containing compound metabolic process 1 Moderately Informative Inherited
Biological Process (BP) cellular protein modification process 1 Moderately Informative Inherited
Biological Process (BP) regulation of gene expression 1 Moderately Informative Inherited
Biological Process (BP) regulation of cellular biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) organ development 1 Moderately Informative Inherited
Biological Process (BP) regulation of protein metabolic process 0.02016 Moderately Informative Inherited
Biological Process (BP) positive regulation of metabolic process 0.384 Moderately Informative Inherited
Biological Process (BP) cellular catabolic process 0.2106 Moderately Informative Inherited
Biological Process (BP) organic substance catabolic process 1 Moderately Informative Inherited
Biological Process (BP) organelle organization 0.2843 Moderately Informative Inherited
Biological Process (BP) anatomical structure morphogenesis 1 Moderately Informative Inherited
Biological Process (BP) cell differentiation 1 Moderately Informative Inherited
Biological Process (BP) regulation of localization 0.5961 Moderately Informative Inherited
Biological Process (BP) regulation of cellular component organization 0.4403 Moderately Informative Inherited
Biological Process (BP) macromolecule localization 0.09004 Moderately Informative Inherited
Biological Process (BP) organic substance transport 0.9008 Moderately Informative Inherited
Biological Process (BP) regulation of multicellular organismal process 0.8879 Moderately Informative Inherited
Biological Process (BP) positive regulation of response to stimulus 0.1177 Moderately Informative Inherited
Biological Process (BP) positive regulation of cellular process 0.5239 Moderately Informative Inherited
Biological Process (BP) regulation of signal transduction 0.07104 Moderately Informative Inherited
Biological Process (BP) signal transduction 0.2296 Moderately Informative Inherited
Biological Process (BP) RNA metabolic process 0.1613 Moderately Informative Inherited
Biological Process (BP) gene expression 0.2816 Moderately Informative Inherited
Biological Process (BP) regulation of biological quality 0.08199 Moderately Informative Inherited
Biological Process (BP) cellular component biogenesis 0.1674 Moderately Informative Inherited
Biological Process (BP) embryonic organ development 0.000444 Informative Direct
Biological Process (BP) secretion by cell 6.871e-13 Informative Direct
Biological Process (BP) vesicle-mediated transport 3.532e-12 Informative Direct
Biological Process (BP) synaptic transmission 2.21e-11 Informative Direct
Biological Process (BP) protein transport 6.468e-09 Informative Direct
Biological Process (BP) cellular membrane organization 0.0001637 Informative Direct
Biological Process (BP) positive regulation of protein metabolic process 0.0003316 Informative Direct
Biological Process (BP) RNA processing 0.0005274 Informative Direct
Biological Process (BP) positive regulation of signal transduction 0.0008607 Informative Direct
Biological Process (BP) regulation of vesicle-mediated transport 0.0008845 Informative Direct
Biological Process (BP) negative regulation of developmental process 0.009933 Informative Inherited
Biological Process (BP) negative regulation of signaling 0.1989 Informative Inherited
Biological Process (BP) negative regulation of cell communication 0.2041 Informative Inherited
Biological Process (BP) negative regulation of response to stimulus 0.2632 Informative Inherited
Biological Process (BP) protein localization to organelle 0.9745 Informative Inherited
Biological Process (BP) dephosphorylation 0.07065 Informative Inherited
Biological Process (BP) regulation of transcription from RNA polymerase II promoter 1 Informative Inherited
Biological Process (BP) organelle localization 0.003728 Informative Inherited
Biological Process (BP) transmembrane transport 0.002857 Informative Inherited
Biological Process (BP) cellular macromolecular complex assembly 0.0032 Informative Inherited
Biological Process (BP) cellular macromolecule catabolic process 0.153 Informative Inherited
Biological Process (BP) protein catabolic process 0.1765 Informative Inherited
Biological Process (BP) proteolysis 0.3267 Informative Inherited
Biological Process (BP) cytoskeleton organization 0.4217 Informative Inherited
Biological Process (BP) anatomical structure formation involved in morphogenesis 0.9274 Informative Inherited
Biological Process (BP) enzyme linked receptor protein signaling pathway 0.06824 Informative Inherited
Biological Process (BP) cytoplasmic transport 1 Informative Inherited
Biological Process (BP) nucleic acid phosphodiester bond hydrolysis 0.00185 Informative Inherited
Biological Process (BP) embryo development ending in birth or egg hatching 0.01696 Informative Inherited
Biological Process (BP) actin filament-based process 0.01574 Informative Inherited
Biological Process (BP) establishment of synaptic vesicle localization 0 Highly Informative Direct
Biological Process (BP) regulation of neurotransmitter levels 0 Highly Informative Direct
Biological Process (BP) vesicle organization 1.271e-13 Highly Informative Direct
Biological Process (BP) neurotransmitter transport 7.937e-13 Highly Informative Direct
Biological Process (BP) autophagy 8.785e-09 Highly Informative Direct
Biological Process (BP) regulation of endocytosis 2.794e-05 Highly Informative Direct
Biological Process (BP) signal release 3.685e-05 Highly Informative Direct
Biological Process (BP) mRNA processing 6.641e-05 Highly Informative Direct
Biological Process (BP) regulation of protein catabolic process 7.245e-05 Highly Informative Direct
Biological Process (BP) transmembrane receptor protein tyrosine kinase signaling pathway 0.0001145 Highly Informative Direct
Biological Process (BP) positive regulation of catabolic process 0.0002866 Highly Informative Direct
Biological Process (BP) negative regulation of cell differentiation 0.001219 Highly Informative Inherited
Biological Process (BP) establishment of protein localization to organelle 0.07216 Highly Informative Inherited
Biological Process (BP) protein dephosphorylation 0.003283 Highly Informative Inherited
Biological Process (BP) protein import 0.001187 Highly Informative Inherited
Biological Process (BP) ubiquitin-dependent protein catabolic process 0.06349 Highly Informative Inherited
Biological Process (BP) Golgi vesicle transport 0.08065 Highly Informative Inherited
Molecular Function (MF) binding 0.0002617 Least Informative Direct
Molecular Function (MF) anion binding 5.913e-06 Moderately Informative Direct
Molecular Function (MF) lipid binding 1.545e-11 Informative Direct
Molecular Function (MF) enzyme binding 0.006224 Informative Inherited
Molecular Function (MF) protein complex binding 0.03069 Highly Informative Inherited
Cellular Component (CC) intracellular organelle part 0.002399 Least Informative Inherited
Cellular Component (CC) intracellular non-membrane-bounded organelle 0.08659 Least Informative Inherited
Cellular Component (CC) protein complex 0.06285 Least Informative Inherited
Cellular Component (CC) membrane 0.07547 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 1 Least Informative Inherited
Cellular Component (CC) cytoplasmic part 0.1153 Least Informative Inherited
Cellular Component (CC) vesicle 1.559e-05 Moderately Informative Direct
Cellular Component (CC) endomembrane system 2.254e-05 Moderately Informative Direct
Cellular Component (CC) cytoskeleton 0.01086 Moderately Informative Inherited
Cellular Component (CC) organelle membrane 0.7355 Moderately Informative Inherited
Cellular Component (CC) nuclear part 0.1676 Moderately Informative Inherited
Cellular Component (CC) intracellular organelle lumen 0.4502 Moderately Informative Inherited
Cellular Component (CC) endosome 8.688e-08 Informative Direct
Cellular Component (CC) cell cortex 8.829e-08 Informative Direct
Cellular Component (CC) coated vesicle 4.385e-07 Informative Direct
Cellular Component (CC) Golgi apparatus 1.708e-05 Informative Direct
Cellular Component (CC) nuclear DNA-directed RNA polymerase complex 6.322e-05 Informative Direct
Cellular Component (CC) actin cytoskeleton 0.002055 Informative Inherited
Cellular Component (CC) nucleoplasm part 0.03363 Informative Inherited
Cellular Component (CC) clathrin-coated vesicle 0 Highly Informative Direct
Cellular Component (CC) cortical cytoskeleton 1.617e-09 Highly Informative Direct
Cellular Component (CC) trans-Golgi network 1.649e-07 Highly Informative Direct
Cellular Component (CC) endosomal part 0.0001576 Highly Informative Direct
Cellular Component (CC) cytoplasmic vesicle membrane 0.5554 Highly Informative Inherited

Document: GO annotation of SCOP domains

Mouse Phenotype (MP)

(show details)
MP termFDR (all)SDMP levelAnnotation (direct or inherited)
Mammalian Phenotype (MP)growth/size/body phenotype0.01424Least InformativeInherited
Mammalian Phenotype (MP)abnormal homeostasis0.9468Least InformativeInherited
Mammalian Phenotype (MP)abnormal postnatal growth/weight/body size0.3762Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal circulating glucose level0.05637InformativeInherited
Mammalian Phenotype (MP)decreased body size0.07503InformativeInherited
Mammalian Phenotype (MP)abnormal total tissue mass0.7261InformativeInherited
Mammalian Phenotype (MP)postnatal growth retardation1.404e-05Highly InformativeDirect
Mammalian Phenotype (MP)decreased birth weight0.0007303Highly InformativeDirect
Mammalian Phenotype (MP)hypoglycemia0.0008709Highly InformativeDirect

Document: MP annotation of SCOP domains

Worm Phenotype (WP)

(show details)
WP termFDR (all)SDWP levelAnnotation (direct or inherited)
Worm Phenotype (WP)growth variant0Least InformativeDirect
Worm Phenotype (WP)cell physiology variant0.0006634Least InformativeDirect
Worm Phenotype (WP)organism environmental stimulus response variant0.1134Least InformativeInherited
Worm Phenotype (WP)endocytic transport defect0.005458Moderately InformativeInherited
Worm Phenotype (WP)chemical response variant0.005993Moderately InformativeInherited
Worm Phenotype (WP)drug resistant0.1295InformativeInherited
Worm Phenotype (WP)coelomocyte uptake defective4.753e-06Highly InformativeDirect
Worm Phenotype (WP)aldicarb resistant0.0002594Highly InformativeDirect

Document: WP annotation of SCOP domains

Yeast Phenotype (YP)

(show details)
YP termFDR (all)SDYP levelAnnotation (direct or inherited)
Yeast Phenotype (YP)intracellular transport0.0009249InformativeDirect

Document: YP annotation of SCOP domains

Fly Anatomy (FA)

(show details)
FA termFDR (all)SDFA levelAnnotation (direct or inherited)
Fly Anatomy (FA)multi-tissue structure0.4353Least InformativeInherited
Fly Anatomy (FA)larva0.5385Least InformativeInherited
Fly Anatomy (FA)cell0.7358Least InformativeInherited
Fly Anatomy (FA)epithelium0.1845Moderately InformativeInherited
Fly Anatomy (FA)developing material anatomical entity0.3402Moderately InformativeInherited
Fly Anatomy (FA)epithelial cell0.002863InformativeInherited
Fly Anatomy (FA)imaginal precursor0.01963InformativeInherited
Fly Anatomy (FA)prepupa0.02312InformativeInherited
Fly Anatomy (FA)pupa0.02706InformativeInherited
Fly Anatomy (FA)cuboidal/columnar epithelium0.09821InformativeInherited

Document: FA annotation of SCOP domains

Xenopus Anatomy (XA)

(show details)
XA termFDR (all)SDXA levelAnnotation (direct or inherited)
Xenopus ANatomical entity (XAN)viscus0Least InformativeDirect

Document: XA annotation of SCOP domains

Arabidopsis Plant Ontology (AP)

(show details) Document: AP annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processTransport0Least InformativeDirect
Biological processProtein transport0Moderately InformativeDirect
Biological processEndocytosis0InformativeDirect
Cellular componentMembrane0Least InformativeDirect
Cellular componentGolgi apparatus0Moderately InformativeDirect
Cellular componentEndosome0Moderately InformativeDirect
Cellular componentCytoplasmic vesicle0Moderately InformativeDirect
Cellular componentCoated pit0Highly InformativeDirect
DomainZinc-finger2.397e-06Moderately InformativeDirect
DomainCoiled coil6.843e-05Moderately InformativeDirect
DomainSH3 domain0InformativeDirect
Molecular functionZinc0.0007406Least InformativeDirect
Molecular functionLipid-binding0InformativeDirect
Molecular functionActin-binding1.139e-06InformativeDirect
Post-translational modificationPhosphoprotein0Least InformativeDirect
Post-translational modificationAcetylation0.0005161Least InformativeDirect
Post-translational modificationUbl conjugation6.396e-08Moderately InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR008942 SSF48464 Protein matches
Abstract

This entry represents domains with a multi-helical, alpha-alpha 2-layered structural fold as found in: the ENTH domain of Epsin; the VHS domain of Hrs, Tom1, and ADP-ribosylation factors; the RPR domain of PCF11 protein; and the N-terminal domain of phosphoinositide-binding clathrin adaptor.

The epsin NH2-terminal homology (ENTH) domain is a membrane interacting module composed of a superhelix of alpha-helices. It is present at the NH2-terminus of proteins that often contain consensus sequences for binding to clathrin coat components and their accessory factors, and therefore function as endocytic adaptors. ENTH domain containing proteins have additional roles in signalling and actin regulation and may have yet other actions in the nucleus. The ENTH domain is structurally similar to the VHS domain.

The ENTH domain is approximately 150 amino acids long. The ENTH domain forms a compact globular structure, composed of eight alpha-helices connected by loops of varying length. Three helical hairpins that are stacked consecutively with a right-handed twist determine the general topology of the domain. This stacking gives the ENTH domain a rectangular appearance when viewed face on. The most highly conserved amino acids fall roughly into two classes: internal residues that are involved in packing and therefore are necessary for structural integrity, and solvent accessible residues that may be involved in protein-protein interactions [PubMed11911874].

VHS domains are found at the N-termini of select proteins involved in intracellular membrane trafficking. The domain consists of eight helices arranged in a superhelix. The surface of the domain has two main features: a basic patch on one side due to several conserved positively charged residues on helix 3 and a negatively charged ridge on the opposite side, formed by residues on helix 2. Comparison of the two VHS domains and the ENTH domain reveals a conserved surface, composed of helices 2 and 4, that is utilised for protein-protein interactions. In addition, VHS domain-containing proteins are also often localized to membranes. It has therefore been suggested that the conserved positively charged surface of helix 3 in VHS and ENTH domains plays a role in membrane binding [PubMed10985773].


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) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Fly Anatomy (FA) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · 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 10 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 ENTH/VHS domain 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 10 hidden Markov models representing the ENTH/VHS domain 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) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Fly Anatomy (FA) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · UniProtKB KeyWords (KW) · Internal database links ]