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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 0 127
Proteins 30,833 0 122


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 system0.5805Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the skeletal system0.7012Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of connective tissue0.1907Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of immune system physiology0.434Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the abdominal organs0.6143Moderately InformativeInherited
Phenotypic Abnormality (PA)Recurrent infections0.1011InformativeInherited
Phenotypic Abnormality (PA)Increased inflammatory response1InformativeInherited
Phenotypic Abnormality (PA)Cellulitis0.00003625Highly 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 phenotype0.00866Least InformativeInherited
Mammalian Phenotype (MP)immune system phenotype0.03634Least InformativeInherited
Mammalian Phenotype (MP)nervous system phenotype0.05307Least InformativeInherited
Mammalian Phenotype (MP)cardiovascular system phenotype0.7491Least InformativeInherited
Mammalian Phenotype (MP)abnormal immune serum protein physiology0.0722Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal nervous system physiology0.08924Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal leukocyte physiology0.1453Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal mononuclear cell morphology0.1668Moderately InformativeInherited
Mammalian Phenotype (MP)hearing/vestibular/ear phenotype0.1893Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal blood cell morphology/development0.2777Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal blood vessel morphology0.4719Moderately 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 metabolism0.9609Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal B cell proliferation0.0002542InformativeDirect
Mammalian Phenotype (MP)abnormal cerebral hemisphere morphology0.0887InformativeInherited
Mammalian Phenotype (MP)abnormal limbic system morphology0.1104InformativeInherited
Mammalian Phenotype (MP)abnormal enzyme/coenzyme activity0.2817InformativeInherited
Mammalian Phenotype (MP)abnormal neuron physiology0.2893InformativeInherited
Mammalian Phenotype (MP)abnormal cochlear hair cell morphology0.3748InformativeInherited
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 amplitude0.0004912Highly InformativeDirect
Mammalian Phenotype (MP)abnormal hippocampus pyramidal cell layer0.0009184Highly InformativeDirect
Mammalian Phenotype (MP)abnormal granulocyte physiology0.05871Highly InformativeInherited
Mammalian Phenotype (MP)abnormal cochlear hair cell stereociliary bundle morphology0.08362Highly 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 variant0.0000004472Least InformativeDirect
Worm Phenotype (WP)organ system morphology variant0.00002177Least InformativeDirect
Worm Phenotype (WP)cell physiology variant0.00008575Least InformativeDirect
Worm Phenotype (WP)organism behavior variant0.008654Least InformativeInherited
Worm Phenotype (WP)organism environmental stimulus response variant0.03402Least InformativeInherited
Worm Phenotype (WP)organism metabolism processing variant0.04801Least InformativeInherited
Worm Phenotype (WP)protein expression variant0.00000004045Moderately InformativeDirect
Worm Phenotype (WP)apoptosis variant0.00003266Moderately InformativeDirect
Worm Phenotype (WP)chemical response variant0.01718Moderately InformativeInherited
Worm Phenotype (WP)cell component morphology variant0.06951Moderately InformativeInherited
Worm Phenotype (WP)germ cell morphology variant0.3699Moderately InformativeInherited
Worm Phenotype (WP)muscle cell physiology variant0.00000000002341InformativeDirect
Worm Phenotype (WP)body wall muscle sarcomere morphology variant0.0000000000573InformativeDirect
Worm Phenotype (WP)mitochondria morphology variant0.00002244InformativeDirect
Worm Phenotype (WP)aldicarb response variant0.0000637InformativeDirect
Worm Phenotype (WP)level of protein expression variant0.0168InformativeInherited
Worm Phenotype (WP)organelle organization biogenesis variant0.2053InformativeInherited
Worm Phenotype (WP)protein modification variant0.5375InformativeInherited
Worm Phenotype (WP)oocyte morphology variant0.9901InformativeInherited
Worm Phenotype (WP)protein expression reduced0.0000000001139Highly InformativeDirect
Worm Phenotype (WP)body elongation variant0.0002283Highly InformativeDirect
Worm Phenotype (WP)endomitotic oocytes0.0004129Highly InformativeDirect
Worm Phenotype (WP)mitochondria alignment variant0.000488Highly InformativeDirect
Worm Phenotype (WP)ovulation variant0.0006493Highly InformativeDirect
Worm Phenotype (WP)protein phosphorylation variant0.0006565Highly InformativeDirect
Worm Phenotype (WP)cytoskeleton organization biogenesis variant0.0364Highly 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)
FA termFDR (all)SDFA levelAnnotation (direct or inherited)
Fly Anatomy (FA)cell component0.0009247InformativeDirect

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 kinases0.00006061Moderately 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 transferase0.000000003278InformativeDirect
Enzyme Commission (EC)Phosphoric diester hydrolases0.00000001441InformativeDirect
Enzyme Commission (EC)Hexosyltransferases0.00008556InformativeDirect
Enzyme Commission (EC)Non-specific protein-tyrosine kinase0Highly InformativeDirect
Enzyme Commission (EC)Phosphoinositide phospholipase C0Highly InformativeDirect

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processTransport0.377Least InformativeInherited
Biological processImmunity0Moderately InformativeDirect
Biological processProtein transport0Moderately InformativeDirect
Biological processDifferentiation0.00000000009459Moderately InformativeDirect
Biological processApoptosis0.00000000107Moderately InformativeDirect
Biological processCell cycle0.001018Moderately InformativeInherited
Biological processIon transport0.7017Moderately InformativeInherited
Biological processEndocytosis0InformativeDirect
Biological processStress response0InformativeDirect
Biological processCell adhesion0.00000000001915InformativeDirect
Biological processNeurogenesis0.0000000004214InformativeDirect
Biological processMitosis0.000000003505InformativeDirect
Biological processInflammatory response0.00001364InformativeDirect
Biological processAutophagy0.0003317InformativeDirect
Biological processCalcium transport0Highly InformativeDirect
Biological processPhagocytosis0.0000000000004989Highly InformativeDirect
Biological processCilium biogenesis/degradation0.000000001007Highly InformativeDirect
Biological processAdaptive immunity0.000000001366Highly InformativeDirect
Biological processExocytosis0.000000742Highly InformativeDirect
Cellular componentMembrane0Least InformativeDirect
Cellular componentCytoplasm0Least InformativeDirect
Cellular componentCytoskeleton0Moderately InformativeDirect
Cellular componentGolgi apparatus0Moderately InformativeDirect
Cellular componentCell junction0Moderately InformativeDirect
Cellular componentCell projection0Moderately InformativeDirect
Cellular componentEndosome0Moderately InformativeDirect
Cellular componentCytoplasmic vesicle0Moderately InformativeDirect
Cellular componentCell membrane0.000000003706Moderately InformativeDirect
Cellular componentLysosome0.00001497InformativeDirect
Cellular componentCoated pit0Highly InformativeDirect
Coding sequence diversityAlternative splicing0.000000001579Least InformativeDirect
Coding sequence diversityChromosomal rearrangement0.00009953InformativeDirect
DiseaseProto-oncogene0Moderately InformativeDirect
DomainRepeat0.0000002436Least InformativeDirect
DomainCoiled coil0Moderately InformativeDirect
DomainSH2 domain0InformativeDirect
DomainSH3 domain0InformativeDirect
DomainSH3-binding0InformativeDirect
DomainANK repeat0.000000006335InformativeDirect
Molecular functionLipid-binding0Moderately InformativeDirect
Molecular functionCalcium0.000002175Moderately InformativeDirect
Post-translational modificationTransferase1Least InformativeInherited
Post-translational modificationKinase0Moderately InformativeDirect
Post-translational modificationDevelopmental protein0.00000006842Moderately InformativeDirect
Post-translational modificationActin-binding0InformativeDirect
Post-translational modificationCalmodulin-binding0InformativeDirect
Post-translational modificationGTPase activation0InformativeDirect
Post-translational modificationGuanine-nucleotide releasing factor0InformativeDirect
Post-translational modificationIon channel0.00000231InformativeDirect
Post-translational modificationCalcium channel0Highly InformativeDirect
Post-translational modificationMyosin0Highly InformativeDirect
Post-translational modificationTyrosine-protein kinase0Highly InformativeDirect
Post-translational modificationVoltage-gated channel0.0000000000001302Highly InformativeDirect
Post-translational modificationActin capping0.0000000132Highly InformativeDirect
Post-translational modificationPhosphoprotein0Least InformativeDirect
Post-translational modificationMyristate0InformativeDirect

Document: KW 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) · 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 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) · UniProtKB KeyWords (KW) · Internal database links ]