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SH3-domain superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   All beta proteins [ 48724] (174)
Fold:   SH3-like barrel [ 50036] (21)
Superfamily:   SH3-domain [ 50044]
Families:   SH3-domain [ 50045] (39)


Superfamily statistics
Genomes (733) Uniprot 2018_03 genome PDB chains (SCOP 1.75)
Domains 39,669 125,642 127
Proteins 30,833 97,806 122


Functional annotation
General category Regulation
Detailed category Signal transduction

Document:
Function annotation of SCOP domain superfamilies

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEO levelAnnotation (direct or inherited)
Enzyme Commission (EC)Acting on ester bonds0.4052Least InformativeInherited
Enzyme Commission (EC)Phosphoric diester hydrolases0.00000006272Moderately InformativeDirect
Enzyme Commission (EC)Protein-serine/threonine kinases0.0001767Moderately InformativeDirect
Enzyme Commission (EC)Glycosyltransferases1Moderately InformativeInherited
Enzyme Commission (EC)Non-specific protein-tyrosine kinase0InformativeDirect
Enzyme Commission (EC)Phosphoinositide phospholipase C0.000000000000003251InformativeDirect
Enzyme Commission (EC)Mitogen-activated protein kinase kinase kinase0.0000000000002472Highly 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 the digestive system0.5967Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of immune system physiology0.4438Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the abdominal organs0.6022Moderately InformativeInherited
Phenotypic Abnormality (PA)Recurrent infections0.1048InformativeInherited
Phenotypic Abnormality (PA)Cellulitis0.00003602Highly InformativeDirect

Document: HP annotation of SCOP domains

Mouse Phenotype (MP)

(show details)
MP termFDR (all)SDMP levelAnnotation (direct or inherited)
Mammalian Phenotype (MP)hematopoietic system phenotype0.008629Least InformativeInherited
Mammalian Phenotype (MP)immune system phenotype0.03625Least InformativeInherited
Mammalian Phenotype (MP)nervous system phenotype0.05296Least InformativeInherited
Mammalian Phenotype (MP)cardiovascular system phenotype0.7488Least InformativeInherited
Mammalian Phenotype (MP)abnormal immune serum protein physiology0.07222Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal nervous system physiology0.08924Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal leukocyte physiology0.1454Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal mononuclear cell morphology0.1667Moderately InformativeInherited
Mammalian Phenotype (MP)hearing/vestibular/ear phenotype0.1892Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal blood cell morphology/development0.2777Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal blood vessel morphology0.4717Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal brain morphology0.5901Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal blood cell morphology0.7992Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal somatic nervous system morphology0.8109Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal professional antigen presenting cell physiology0.8151Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal metabolism0.9608Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal B cell proliferation0.000254InformativeDirect
Mammalian Phenotype (MP)abnormal cerebral hemisphere morphology0.0887InformativeInherited
Mammalian Phenotype (MP)abnormal limbic system morphology0.1104InformativeInherited
Mammalian Phenotype (MP)abnormal enzyme/coenzyme activity0.2816InformativeInherited
Mammalian Phenotype (MP)abnormal neuron physiology0.2893InformativeInherited
Mammalian Phenotype (MP)abnormal cochlear hair cell morphology0.3746InformativeInherited
Mammalian Phenotype (MP)abnormal interleukin secretion0.3885InformativeInherited
Mammalian Phenotype (MP)abnormal T cell differentiation0.4025InformativeInherited
Mammalian Phenotype (MP)abnormal effector T cell morphology0.4621InformativeInherited
Mammalian Phenotype (MP)abnormal alpha-beta T cell morphology0.5157InformativeInherited
Mammalian Phenotype (MP)abnormal synaptic vesicle recycling0.000008222Highly InformativeDirect
Mammalian Phenotype (MP)abnormal interleukin-2 secretion0.0004402Highly InformativeDirect
Mammalian Phenotype (MP)decreased excitatory postsynaptic current amplitude0.000491Highly InformativeDirect
Mammalian Phenotype (MP)abnormal hippocampus pyramidal cell layer0.0009178Highly InformativeDirect
Mammalian Phenotype (MP)abnormal granulocyte physiology0.05871Highly InformativeInherited
Mammalian Phenotype (MP)abnormal cochlear hair cell stereociliary bundle morphology0.08358Highly InformativeInherited
Mammalian Phenotype (MP)abnormal CD8-positive, alpha beta T cell morphology0.2801Highly InformativeInherited

Document: MP annotation of SCOP domains

Worm Phenotype (WP)

(show details)
WP termFDR (all)SDWP levelAnnotation (direct or inherited)
Worm Phenotype (WP)cell morphology variant0.0000001966Least InformativeDirect
Worm Phenotype (WP)organ system morphology variant0.00001016Least InformativeDirect
Worm Phenotype (WP)cell physiology variant0.00004462Least InformativeDirect
Worm Phenotype (WP)organism behavior variant0.01127Least InformativeInherited
Worm Phenotype (WP)organism metabolism processing variant0.0359Least InformativeInherited
Worm Phenotype (WP)organism environmental stimulus response variant0.04192Least InformativeInherited
Worm Phenotype (WP)protein expression variant0.00000001389Moderately InformativeDirect
Worm Phenotype (WP)apoptosis variant0.00004098Moderately InformativeDirect
Worm Phenotype (WP)chemical response variant0.01709Moderately InformativeInherited
Worm Phenotype (WP)cell component morphology variant0.05031Moderately InformativeInherited
Worm Phenotype (WP)germ cell morphology variant0.5318Moderately InformativeInherited
Worm Phenotype (WP)muscle cell physiology variant0.000000000002626InformativeDirect
Worm Phenotype (WP)body wall muscle sarcomere morphology variant0.000000000007756InformativeDirect
Worm Phenotype (WP)mitochondria morphology variant0.000007716InformativeDirect
Worm Phenotype (WP)aldicarb response variant0.00007483InformativeDirect
Worm Phenotype (WP)level of protein expression variant0.01062InformativeInherited
Worm Phenotype (WP)organelle organization biogenesis variant0.2018InformativeInherited
Worm Phenotype (WP)protein modification variant0.5812InformativeInherited
Worm Phenotype (WP)oocyte morphology variant0.9895InformativeInherited
Worm Phenotype (WP)protein expression reduced0.00000000001197Highly InformativeDirect
Worm Phenotype (WP)body elongation variant0.000243Highly InformativeDirect
Worm Phenotype (WP)mitochondria alignment variant0.0002716Highly InformativeDirect
Worm Phenotype (WP)endomitotic oocytes0.0004386Highly InformativeDirect
Worm Phenotype (WP)ovulation variant0.0006434Highly InformativeDirect
Worm Phenotype (WP)protein phosphorylation variant0.0007076Highly InformativeDirect
Worm Phenotype (WP)cytoskeleton organization biogenesis variant0.03633Highly InformativeInherited

Document: WP annotation of SCOP domains

Yeast Phenotype (YP)

(show details)
YP termFDR (all)SDYP levelAnnotation (direct or inherited)
Yeast Phenotype (YP)morphology0.1479Moderately InformativeInherited
Yeast Phenotype (YP)intracellular transport0.00002122InformativeDirect
Yeast Phenotype (YP)subcellular morphology0.3141InformativeInherited
Yeast Phenotype (YP)chitin deposition0.0003522Highly InformativeDirect

Document: YP annotation of SCOP domains

Fly Phenotype (FP)

(show details) Document: FP annotation of SCOP domains

Fly Anatomy (FA)

(show details) 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)whole plant0Least InformativeDirect
Plant ANatomical entity (PAN)guard cell0Least InformativeDirect
Plant ANatomical entity (PAN)seed0Least InformativeDirect
Plant ANatomical entity (PAN)portion of meristem tissue0Least InformativeDirect
Plant ANatomical entity (PAN)megasporophyll0Least InformativeDirect
Plant ANatomical entity (PAN)microsporophyll0Least InformativeDirect
Plant ANatomical entity (PAN)flower0Least InformativeDirect
Plant ANatomical entity (PAN)inflorescence0Least InformativeDirect
Plant ANatomical entity (PAN)collective phyllome structure0Least InformativeDirect
Plant ANatomical entity (PAN)root system0Least InformativeDirect
Plant ANatomical entity (PAN)shoot axis0Least InformativeDirect
Plant ANatomical entity (PAN)leaf0Least InformativeDirect
Plant ANatomical entity (PAN)sporangium0Least InformativeDirect
Plant ANatomical entity (PAN)cardinal part of multi-tissue plant structure0Least InformativeDirect
Plant ANatomical entity (PAN)inflorescence meristem0Moderately InformativeDirect
Plant ANatomical entity (PAN)cotyledon0Moderately InformativeDirect
Plant structure DEvelopment stage (PDE)4 leaf senescence stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)E expanded cotyledon stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)F mature embryo stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)C globular stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)D bilateral stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.12 twelve leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.08 eight leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.02 two leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.10 ten leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.04 four leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.06 six leaves visible stage0Least InformativeDirect

Document: AP annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEC levelAnnotation (direct or inherited)
Enzyme Commission (EC)Transferring phosphorus-containing groups0Least InformativeDirect
Enzyme Commission (EC)Hydrolases1Least InformativeInherited
Enzyme Commission (EC)Protein-serine/threonine kinases0.00006321Moderately InformativeDirect
Enzyme Commission (EC)Transferring one-carbon groups1Moderately InformativeInherited
Enzyme Commission (EC)Acyltransferases1Moderately InformativeInherited
Enzyme Commission (EC)Glycosyltransferases1Moderately InformativeInherited
Enzyme Commission (EC)Protein-tyrosine kinases0InformativeDirect
Enzyme Commission (EC)RING-type E3 ubiquitin transferase0.000000002244InformativeDirect
Enzyme Commission (EC)Phosphoric diester hydrolases0.00000001418InformativeDirect
Enzyme Commission (EC)Hexosyltransferases0.00008998InformativeDirect
Enzyme Commission (EC)Non-specific protein-tyrosine kinase0Highly InformativeDirect
Enzyme Commission (EC)Phosphoinositide phospholipase C0Highly InformativeDirect

Document: EC annotation of SCOP domains

InterPro annotation
Cross references IPR001452 SSF50044 Protein matches
Abstract SH3 (src Homology-3) domains are small protein modules containing approximately 50 amino acid residues [PubMed15335710, PubMed11256992]. They are found in a great variety of intracellular or membrane-associated proteins [PubMed1639195, PubMed14731533, PubMed7531822] for example, in a variety of proteins with enzymatic activity, in adaptor proteins that lack catalytic sequences and in cytoskeletal proteins, such as fodrin and yeast actin binding protein ABP-1.

The SH3 domain has a characteristic fold which consists of five or six beta-strands arranged as two tightly packed anti-parallel beta sheets. The linker regions may contain short helices. The surface of the SH2-domain bears a flat, hydrophobic ligand-binding pocket which consists of three shallow grooves defined by conservative aromatic residues in which the ligand adopts an extended left-handed helical arrangement. The ligand binds with low affinity but this may be enhanced by multiple interactions. The region bound by the SH3 domain is in all cases proline-rich and contains PXXP as a core-conserved binding motif. The function of the SH3 domain is not well understood but they may mediate many diverse processes such as increasing local concentration of proteins, altering their subcellular location and mediating the assembly of large multiprotein complexes [PubMed7953536].


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 Phenotype (FP) · Fly Anatomy (FA) · Zebrafish Anatomy (ZA) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) ]

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 58 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 SH3-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 58 hidden Markov models representing the SH3-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 · Enzyme Commission (EC) · Human Phenotype (HP) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Fly Phenotype (FP) · Fly Anatomy (FA) · Zebrafish Anatomy (ZA) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · Internal database links ]