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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 system0.7052Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the gastrointestinal tract0.2107Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of connective tissue0.2938Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the abdominal organs0.6211Moderately InformativeInherited
Phenotypic Abnormality (PA)Cellulitis0.000273Highly 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 phenotype0.01011Least InformativeInherited
Mammalian Phenotype (MP)immune system phenotype0.04097Least InformativeInherited
Mammalian Phenotype (MP)nervous system phenotype0.05965Least InformativeInherited
Mammalian Phenotype (MP)cardiovascular system phenotype0.7616Least InformativeInherited
Mammalian Phenotype (MP)abnormal immune serum protein physiology0.07178Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal nervous system physiology0.08773Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal leukocyte physiology0.1455Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal mononuclear cell morphology0.1671Moderately InformativeInherited
Mammalian Phenotype (MP)hearing/vestibular/ear phenotype0.1956Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal blood cell morphology/development0.2772Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal blood vessel morphology0.4816Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal brain morphology0.5853Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal blood cell morphology0.7998Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal professional antigen presenting cell physiology0.8118Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal somatic nervous system morphology0.8126Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal metabolism0.9629Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal B cell proliferation0.0002684InformativeDirect
Mammalian Phenotype (MP)abnormal cerebral hemisphere morphology0.08867InformativeInherited
Mammalian Phenotype (MP)abnormal limbic system morphology0.1104InformativeInherited
Mammalian Phenotype (MP)abnormal enzyme/coenzyme activity0.2852InformativeInherited
Mammalian Phenotype (MP)abnormal neuron physiology0.2893InformativeInherited
Mammalian Phenotype (MP)abnormal CNS synaptic transmission0.3472InformativeInherited
Mammalian Phenotype (MP)abnormal cochlear hair cell morphology0.3784InformativeInherited
Mammalian Phenotype (MP)abnormal interleukin secretion0.3934InformativeInherited
Mammalian Phenotype (MP)abnormal T cell differentiation0.401InformativeInherited
Mammalian Phenotype (MP)abnormal effector T cell morphology0.4637InformativeInherited
Mammalian Phenotype (MP)abnormal alpha-beta T cell morphology0.5172InformativeInherited
Mammalian Phenotype (MP)abnormal synaptic vesicle recycling0.000008205Highly InformativeDirect
Mammalian Phenotype (MP)abnormal interleukin-2 secretion0.0004401Highly InformativeDirect
Mammalian Phenotype (MP)decreased excitatory postsynaptic current amplitude0.0005036Highly InformativeDirect
Mammalian Phenotype (MP)abnormal hippocampus pyramidal cell layer0.0009464Highly InformativeDirect
Mammalian Phenotype (MP)abnormal granulocyte physiology0.05874Highly InformativeInherited
Mammalian Phenotype (MP)abnormal cochlear hair cell stereociliary bundle morphology0.08477Highly InformativeInherited
Mammalian Phenotype (MP)abnormal CD8-positive, alpha beta T cell morphology0.2822Highly 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 variant0.000002652Least InformativeDirect
Worm Phenotype (WP)organ system morphology variant0.00002196Least InformativeDirect
Worm Phenotype (WP)cell physiology variant0.00003307Least InformativeDirect
Worm Phenotype (WP)organism environmental stimulus response variant0.02718Least InformativeInherited
Worm Phenotype (WP)organism behavior variant0.02821Least InformativeInherited
Worm Phenotype (WP)organism metabolism processing variant0.09964Least InformativeInherited
Worm Phenotype (WP)protein expression variant0.000000006948Moderately InformativeDirect
Worm Phenotype (WP)apoptosis variant0.00005179Moderately InformativeDirect
Worm Phenotype (WP)metabolic pathway variant0.01422Moderately InformativeInherited
Worm Phenotype (WP)drug response variant0.1043Moderately InformativeInherited
Worm Phenotype (WP)cell organization biogenesis variant0.5881Moderately InformativeInherited
Worm Phenotype (WP)cell homeostasis metabolism variant0.9209Moderately InformativeInherited
Worm Phenotype (WP)germ cell morphology variant0.9872Moderately InformativeInherited
Worm Phenotype (WP)body wall muscle sarcomere morphology variant0.000000000009738InformativeDirect
Worm Phenotype (WP)muscle cell physiology variant0.0000000003423InformativeDirect
Worm Phenotype (WP)mitochondria morphology variant0.0000003152InformativeDirect
Worm Phenotype (WP)cell component localization variant0.00002954InformativeDirect
Worm Phenotype (WP)aldicarb response variant0.0001217InformativeDirect
Worm Phenotype (WP)coelomic system physiology variant0.0002376InformativeDirect
Worm Phenotype (WP)cytoskeleton organization biogenesis variant0.005956InformativeInherited
Worm Phenotype (WP)level of protein expression variant0.008832InformativeInherited
Worm Phenotype (WP)protein modification variant0.4289InformativeInherited
Worm Phenotype (WP)oocyte morphology variant0.9778InformativeInherited
Worm Phenotype (WP)protein expression reduced0.00000000001619Highly InformativeDirect
Worm Phenotype (WP)actin organization biogenesis variant0.00006661Highly InformativeDirect
Worm Phenotype (WP)body elongation variant0.0002911Highly InformativeDirect
Worm Phenotype (WP)ovulation variant0.0005149Highly InformativeDirect
Worm Phenotype (WP)endomitotic oocytes0.0005919Highly InformativeDirect
Worm Phenotype (WP)protein phosphorylation variant0.0007248Highly InformativeDirect

Document: WP annotation of SCOP domains

Yeast Phenotype (YP)

(show details)
YP termFDR (all)SDYP levelAnnotation (direct or inherited)
Yeast Phenotype (YP)morphology0.1488Moderately InformativeInherited
Yeast Phenotype (YP)intracellular transport0.00002112InformativeDirect
Yeast Phenotype (YP)subcellular morphology0.3133InformativeInherited
Yeast Phenotype (YP)chitin deposition0.0003534Highly InformativeDirect

Document: YP annotation of SCOP domains

Fly Phenotype (FP)

(show details) Document: FP annotation of SCOP domains

Fly Anatomy (FA)

(show details)
FA termFDR (all)SDFA levelAnnotation (direct or inherited)
Fly Anatomy (FA)cell component0.0009574InformativeDirect

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 ANatomical entity (PAN)pollen0Moderately 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)Aminoacyltransferases0.00000003751Moderately InformativeDirect
Enzyme Commission (EC)Protein-serine/threonine kinases0.00003455Moderately InformativeDirect
Enzyme Commission (EC)Transferring one-carbon groups1Moderately InformativeInherited
Enzyme Commission (EC)Glycosyltransferases1Moderately InformativeInherited
Enzyme Commission (EC)Protein-tyrosine kinases0InformativeDirect
Enzyme Commission (EC)RING-type E3 ubiquitin transferase0.0000000000245InformativeDirect
Enzyme Commission (EC)Phosphoric diester hydrolases0.0000000006559InformativeDirect
Enzyme Commission (EC)Hexosyltransferases0.000111InformativeDirect
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 171 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 171 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 ]