3U23

Atomic resolution crystal structure of the 2nd SH3 domain from human CD2AP (CMS) in complex with a proline-rich peptide from human RIN3

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations
Protein Modification Annotation

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	SH3-domain	8090114	3000153	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	SH3_1	e3u23A1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: SH3_1	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.30.30.40	Mainly Beta	Roll	SH3 type barrels.	SH3 Domains	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF07653	Variant SH3 domain (SH3_2)	Variant SH3 domain	SH3 (Src homology 3) domains are often indicative of a protein involved in signal transduction related to cytoskeletal organisation. First described in the Src cytoplasmic tyrosine kinase Swiss:P12931. The structure is a partly opened beta barrel.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	CD2-associated protein	cytoskeletal protein binding actin binding protein-containing complex binding protein binding binding actin filament binding SH3 domain binding protein domain specific binding cell adhesion molecule binding cadherin binding identical protein binding structural constituent of cytoskeleton structural molecule activity	developmental process multicellular organismal process gonad development reproductive system development reproductive process sex differentiation animal organ development developmental process involved in reproduction male gonad development male sex differentiation multicellular organism development development of primary male sexual characteristics development of primary sexual characteristics anatomical structure development reproductive structure development developmental process multicellular organismal process gonad development reproductive system development reproductive process sex differentiation animal organ development developmental process involved in reproduction male gonad development male sex differentiation multicellular organism development development of primary male sexual characteristics development of primary sexual characteristics anatomical structure development reproductive structure development system development cellular process cell division apoptotic process cell death programmed cell death organonitrogen compound catabolic process organonitrogen compound metabolic process catabolic process primary metabolic process protein catabolic process macromolecule catabolic process organic substance metabolic process metabolic process protein metabolic process macromolecule metabolic process organic substance catabolic process cellular component organization cellular component biogenesis cellular component assembly protein-containing complex organization protein complex oligomerization protein-containing complex assembly cellular component organization or biogenesis protein heterooligomerization cell migration cell motility organelle organization actin cytoskeleton organization actin filament organization actin filament-based process supramolecular fiber organization cytoskeleton organization kidney development renal system development protein localization regulation of localization regulation of biological process cellular localization regulation of cellular process regulation of protein localization positive regulation of protein localization to nucleus biological regulation positive regulation of biological process regulation of protein localization to nucleus protein localization to nucleus localization regulation of cellular localization cellular macromolecule localization macromolecule localization protein localization to organelle positive regulation of protein localization positive regulation of cellular process cellular response to stimulus immune response-regulating cell surface receptor signaling pathway response to stimulus signaling cell communication positive regulation of response to stimulus immune response-activating signaling pathway immune response-regulating signaling pathway positive regulation of immune response regulation of immune system process signal transduction positive regulation of immune system process cell surface receptor signaling pathway immune response-activating cell surface receptor signaling pathway immune response T cell receptor signaling pathway regulation of response to stimulus immune system process regulation of immune response antigen receptor-mediated signaling pathway activation of immune response intracellular signal transduction intracellular signaling cassette phosphatidylinositol 3-kinase/protein kinase B signal transduction stress-activated MAPK cascade stress-activated protein kinase signaling cascade cellular response to stress response to stress MAPK cascade transforming growth factor beta1 production cellular biosynthetic process cellular metabolic process gene expression macromolecule biosynthetic process biosynthetic process cytokine production organic substance biosynthetic process transforming growth factor beta production regulation of cytoskeleton organization regulation of cellular component organization regulation of actin filament-based process regulation of organelle organization regulation of actin cytoskeleton organization response to transforming growth factor beta response to endogenous stimulus response to growth factor small GTPase-mediated signal transduction negative regulation of signaling regulation of small GTPase mediated signal transduction negative regulation of intracellular signal transduction negative regulation of biological process regulation of signal transduction negative regulation of cell communication regulation of intracellular signal transduction negative regulation of cellular process regulation of signaling negative regulation of response to stimulus negative regulation of small GTPase mediated signal transduction negative regulation of signal transduction regulation of cell communication cell junction organization synapse organization regulation of transforming growth factor beta production regulation of transforming growth factor beta1 production negative regulation of cellular metabolic process regulation of cytokine production regulation of multicellular organismal process negative regulation of macromolecule metabolic process regulation of biosynthetic process negative regulation of transforming growth factor beta1 production negative regulation of metabolic process regulation of cellular metabolic process negative regulation of cytokine production regulation of macromolecule metabolic process negative regulation of cellular biosynthetic process negative regulation of transforming growth factor beta production regulation of cellular biosynthetic process regulation of gene expression negative regulation of gene expression negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process regulation of macromolecule biosynthetic process negative regulation of multicellular organismal process regulation of metabolic process substrate-dependent cell migration, cell extension plasma membrane bounded cell projection organization cell projection organization plasma membrane bounded cell projection assembly substrate-dependent cell migration cell projection assembly cell cycle establishment of protein localization nitrogen compound transport transport positive regulation of establishment of protein localization positive regulation of secretion by cell protein localization to extracellular region positive regulation of protein transport regulation of secretion by cell secretion by cell positive regulation of secretion regulation of transport secretion organic substance transport regulation of establishment of protein localization establishment of protein localization to extracellular region export from cell regulation of protein transport protein secretion establishment of localization positive regulation of protein secretion regulation of protein secretion regulation of secretion positive regulation of transport protein transport immunological synapse formation cell-cell recognition cell activation cell recognition lymphocyte activation leukocyte activation defense response inflammatory response	cell-cell junction anchoring junction cell junction cellular anatomical entity intracellular organelle intracellular anatomical structure podosome cytoskeleton organelle intracellular non-membrane-bounded organelle actin cytoskeleton non-membrane-bounded organelle extracellular exosome membrane-bounded organelle cell-cell junction anchoring junction cell junction cellular anatomical entity intracellular organelle intracellular anatomical structure podosome cytoskeleton organelle intracellular non-membrane-bounded organelle actin cytoskeleton non-membrane-bounded organelle extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region extracellular space vesicle extracellular membrane-bounded organelle cell leading edge somatodendritic compartment cell projection dendrite dendritic tree neuron projection plasma membrane bounded cell projection cytoplasm neuromuscular junction synapse ruffle polymeric cytoskeletal fiber protein-containing complex actin filament filamentous actin supramolecular fiber supramolecular polymer supramolecular complex axon centrosome microtubule organizing center centriolar satellite microtubule cytoskeleton cell periphery plasma membrane membrane nucleus membrane-enclosed lumen intracellular membrane-bounded organelle nucleolus intracellular organelle lumen organelle lumen fibrillar center nuclear lumen endosome intracellular vesicle endomembrane system cytoplasmic vesicle late endosome
B	Ras and Rab interactor 3	small GTPase binding protein binding binding enzyme binding GTPase binding GTPase regulator activity enzyme regulator activity guanyl-nucleotide exchange factor activity nucleoside-triphosphatase regulator activity molecular function regulator activity enzyme activator activity GTPase activator activity molecular function activator activity	cellular component organization regulation of cellular component size regulation of vesicle size biological regulation cellular process cellular component organization or biogenesis regulation of biological quality regulation of anatomical structure size localization import into cell transport endocytosis establishment of localization vesicle-mediated transport cellular component organization regulation of cellular component size regulation of vesicle size biological regulation cellular process cellular component organization or biogenesis regulation of biological quality regulation of anatomical structure size localization import into cell transport endocytosis establishment of localization vesicle-mediated transport cellular response to stimulus negative regulation of locomotion negative regulation of leukocyte chemotaxis regulation of cell motility regulation of cellular process response to stimulus regulation of response to external stimulus negative regulation of biological process negative regulation of chemotaxis taxis negative regulation of cellular process regulation of cell migration myeloid leukocyte migration negative regulation of mast cell chemotaxis cell migration regulation of immune system process cell motility negative regulation of cell migration locomotion regulation of mast cell chemotaxis cell chemotaxis chemotaxis regulation of biological process regulation of leukocyte chemotaxis negative regulation of response to stimulus regulation of leukocyte migration mast cell migration response to external stimulus regulation of chemotaxis leukocyte migration cellular response to chemical stimulus negative regulation of leukocyte migration negative regulation of immune system process regulation of response to stimulus immune system process regulation of locomotion response to chemical negative regulation of response to external stimulus mast cell chemotaxis negative regulation of cell motility leukocyte chemotaxis regulation of localization regulation of cellular component organization receptor internalization negative regulation of transport negative regulation of endocytosis regulation of receptor internalization regulation of endocytosis negative regulation of cellular component organization regulation of transport negative regulation of receptor-mediated endocytosis regulation of receptor-mediated endocytosis regulation of vesicle-mediated transport receptor-mediated endocytosis negative regulation of receptor internalization signaling signal transduction cell communication	membrane-bounded organelle intracellular organelle intracellular anatomical structure cytoplasmic vesicle organelle intracellular vesicle cytoplasm cellular anatomical entity intracellular membrane-bounded organelle vesicle early endosome endosome endomembrane system cytosol membrane-bounded organelle intracellular organelle intracellular anatomical structure cytoplasmic vesicle organelle intracellular vesicle cytoplasm cellular anatomical entity intracellular membrane-bounded organelle vesicle early endosome endosome endomembrane system cytosol somatodendritic compartment cell body neuronal cell body axon cell projection neuron projection plasma membrane bounded cell projection dendrite dendritic tree endocytic vesicle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR036028	SH3-like domain superfamily	Homologous Superfamily
A	IPR035777	CD2-associated protein, third SH3 domain	Domain
A	IPR001452	SH3 domain	Domain
A	IPR035775	CD2-associated protein, first SH3 domain	Domain
A	IPR035776	CD2-associated protein, second SH3 domain	Domain
B	IPR000159	Ras-associating domain	Domain
B	IPR036860	SH2 domain superfamily	Homologous Superfamily
B	IPR035869	Ras and Rab interactor 3, SH2 domain	Domain
B	IPR000980	SH2 domain	Domain
B	IPR037191	VPS9 domain superfamily	Homologous Superfamily
B	IPR045046	Vacuolar protein sorting-associated protein 9-like	Family
B	IPR003123	VPS9 domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	Pharos: Q9Y5K6	Alzheimer disease focal segmental glomerulosclerosis 3, susceptibility to focal segmental glomerulosclerosis plasma cell myeloma spina bifida Acute Confusional Senile Dementia lung adenocarcinoma medulloblastoma pancreatic intraductal papillary-mucinous neoplasm glioblastoma malignant ependymoma ovarian cancer pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia proteinuria atypical teratoid rhabdoid tumor Alzheimer disease focal segmental glomerulosclerosis 3, susceptibility to focal segmental glomerulosclerosis plasma cell myeloma spina bifida Acute Confusional Senile Dementia lung adenocarcinoma medulloblastoma pancreatic intraductal papillary-mucinous neoplasm glioblastoma malignant ependymoma ovarian cancer pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia proteinuria atypical teratoid rhabdoid tumor malignant glioma pancreatic intraductal papillary-mucinous carcinoma
B	Pharos: Q8TB24	bone Paget disease chronic obstructive pulmonary disease adenoma breast carcinoma gastric carcinoma malignant mesothelioma pilocytic astrocytoma astrocytic tumor glioblastoma non-small cell lung carcinoma primary biliary cholangitis colorectal cancer lung carcinoma osteosarcoma

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
B	NH2	RESID: AA0081 , AA0083 , AA0084 , AA0086 , AA0087 , AA0088 , AA0090 , AA0091 , AA0092 , AA0093 , AA0095 , AA0096 , AA0097 , AA0098 , AA0099 , AA0100 PSI-MOD : L-alanine amide MOD:00090 , L-asparagine amide MOD:00092 , L-aspartic acid 1-amide MOD:00093 , L-glutamine amide MOD:00095 , L-glutamic acid 1-amide MOD:00096 , glycine amide MOD:00097 , L-isoleucine amide MOD:00099 , L-leucine amide MOD:00100 , L-lysine amide MOD:00101 , L-methionine amide MOD:00102 , L-proline amide MOD:00104 , L-serine amide MOD:00105 , L-threonine amide MOD:00106 , L-tryptophan amide MOD:00107 , L-tyrosine amide MOD:00108 , L-valine amide MOD:00109

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.