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	PF14604	Variant SH3 domain (SH3_9)	Variant SH3 domain	-	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 clathrin binding phosphatidylinositol 3-kinase binding phosphatidylinositol 3-kinase regulatory subunit binding 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 clathrin binding phosphatidylinositol 3-kinase binding phosphatidylinositol 3-kinase regulatory subunit 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 immune system development lymph node development immune system process hematopoietic or lymphoid organ development cellular process cell division cell population proliferation renal filtration cell differentiation kidney epithelium development cellular developmental process glomerular epithelial cell differentiation epithelial cell differentiation renal system development cell differentiation nephron development nephron epithelium development epithelial cell differentiation involved in kidney development epithelium development glomerular epithelium development tissue development glomerulus development cell differentiation involved in kidney development podocyte differentiation kidney development apoptotic process cell death programmed cell death catabolic process metabolic process primary metabolic process protein catabolic process protein metabolic process macromolecule metabolic process macromolecule 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 cellular response to stimulus regulation of biological process small GTPase-mediated signal transduction regulation of cellular process response to stimulus signaling biological regulation intracellular signal transduction cell communication intracellular signaling cassette Rab protein signal transduction signal transduction renal system process system process renal absorption renal albumin absorption renal protein absorption cell migration cell motility localization localization of cell endothelium development response to stress response to wounding protein localization establishment of protein localization cellular localization nitrogen compound transport transport secretion establishment of protein localization to extracellular region export from cell protein secretion establishment of localization protein localization to extracellular region secretion by cell protein transport cellular macromolecule localization macromolecule localization organelle organization actin cytoskeleton organization actin filament organization actin filament-based process supramolecular fiber organization cytoskeleton organization hepaticobiliary system development gland development liver development cellular response to growth factor stimulus cell surface receptor signaling pathway response to endogenous stimulus cellular response to nerve growth factor stimulus cellular response to endogenous stimulus nerve growth factor signaling pathway neurotrophin signaling pathway response to nerve growth factor response to growth factor regulation of localization regulation of protein localization positive regulation of protein localization to nucleus positive regulation of biological process regulation of protein localization to nucleus protein localization to nucleus regulation of cellular localization protein localization to organelle positive regulation of protein localization positive regulation of cellular process connective tissue development adipose tissue development immune response-regulating cell surface receptor signaling pathway 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 positive regulation of immune system process immune response-activating cell surface receptor signaling pathway immune response T cell receptor signaling pathway regulation of response to stimulus regulation of immune response antigen receptor-mediated signaling pathway activation of immune response phosphatidylinositol 3-kinase/protein kinase B signal transduction stress-activated MAPK cascade stress-activated protein kinase signaling cascade cellular 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 transforming growth factor beta production ERK1 and ERK2 cascade 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 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 protein polymerization actin polymerization or depolymerization actin filament polymerization lipid metabolic process 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 neuron apoptotic process negative regulation of neuron apoptotic process negative regulation of programmed cell death regulation of apoptotic process regulation of programmed cell death negative regulation of apoptotic process regulation of neuron apoptotic 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 adhesion cell-cell adhesion cell-cell adhesion mediated by cadherin axonogenesis developmental growth plasma membrane bounded cell projection morphogenesis cell development neuron projection development cell growth cell morphogenesis neurogenesis cell projection morphogenesis neuron differentiation neuron projection morphogenesis collateral sprouting developmental cell growth growth nervous system development axon development cell morphogenesis involved in neuron differentiation developmental growth involved in morphogenesis generation of neurons anatomical structure morphogenesis neuron development positive regulation of establishment of protein localization positive regulation of secretion by cell positive regulation of protein transport regulation of secretion by cell positive regulation of secretion regulation of transport regulation of establishment of protein localization regulation of protein transport positive regulation of protein secretion regulation of protein secretion regulation of secretion positive regulation of transport filopodium assembly response to hormone response to chemical response to peptide hormone response to insulin response to oxygen-containing compound response to nitrogen compound regulation of synaptic plasticity trans-synaptic signaling modulation of chemical synaptic transmission cell-cell signaling chemical synaptic transmission synaptic signaling regulation of trans-synaptic signaling anterograde trans-synaptic signaling regulation of biological quality membrane organization neurotrophin TRK receptor signaling pathway cell surface receptor protein tyrosine kinase signaling pathway enzyme-linked receptor protein signaling pathway immunological synapse formation cell-cell recognition cell activation cell recognition lymphocyte activation leukocyte activation maintenance of blood-brain barrier multicellular organismal-level homeostasis homeostatic process anatomical structure homeostasis tissue homeostasis biological process involved in interspecies interaction between organisms response to other organism response to external stimulus response to external biotic stimulus response to virus response to biotic stimulus defense response inflammatory response response to oxidative stress response to glial cell derived neurotrophic factor D-glucose import hexose transmembrane transport carbohydrate transport transmembrane transport D-glucose transmembrane transport monosaccharide transmembrane transport carbohydrate transmembrane transport cell-cell junction organization	intracellular organelle intracellular anatomical structure podosome cytoskeleton organelle intracellular non-membrane-bounded organelle cellular anatomical entity actin cytoskeleton non-membrane-bounded organelle extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region intracellular organelle intracellular anatomical structure podosome cytoskeleton organelle intracellular non-membrane-bounded organelle cellular anatomical entity 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 cell junction nucleus membrane-enclosed lumen intracellular membrane-bounded organelle endomembrane system intracellular organelle lumen organelle envelope lumen organelle envelope organelle lumen nuclear envelope lumen nuclear envelope 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-cell junction anchoring junction filtration diaphragm slit diaphragm cell periphery plasma membrane membrane growth cone distal axon site of polarized growth Golgi apparatus subcompartment Golgi apparatus organelle subcompartment trans-Golgi network membrane trans-Golgi network organelle membrane nucleolus fibrillar center nuclear lumen endosome intracellular vesicle 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	IPR050384	Endophilin/SH3RF	Family
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 U.S. National Science Foundation (DBI-2321666), 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 R01GM157729.