2DBM | pdb_00002dbm

Solution structures of the SH3 domain of human SH3-containing GRB2-like protein 2

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
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

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d2dbma1	All beta proteins	SH3-like barrel	SH3-domain	automated matches	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d2dbma3	Artifacts	Tags	Tags	Tags	C-terminal Tags	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d2dbma2	Artifacts	Tags	Tags	Tags	N-terminal Tags	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	SH3-domain	8067917	4000369	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	SH3-domain	8067918	3000153	SCOP2 (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	Transketolase_C	e2dbmA1	A: alpha bundles	X: Profilin-like	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Transketolase_C	ECOD (develop294)

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	SH3-containing GRB2-like protein 2	binding lipid binding identical protein binding protein binding	synaptic vesicle endocytosis import into cell cellular localization transport synaptic vesicle cycle establishment of localization vesicle-mediated transport presynaptic endocytosis vesicle-mediated transport in synapse synaptic vesicle recycling localization establishment of localization in cell cellular process endocytosis synaptic vesicle endocytosis import into cell cellular localization transport synaptic vesicle cycle establishment of localization vesicle-mediated transport presynaptic endocytosis vesicle-mediated transport in synapse synaptic vesicle recycling localization establishment of localization in cell cellular process endocytosis developmental process multicellular organism development multicellular organismal process central nervous system development anatomical structure development nervous system development system development cellular developmental process developmental growth cell projection organization plasma membrane bounded cell projection morphogenesis cell development neuron projection development cell growth cell morphogenesis cellular component organization neurogenesis cell projection morphogenesis neuron differentiation neuron projection morphogenesis cell differentiation cellular component organization or biogenesis dendrite extension neuron projection extension plasma membrane bounded cell projection organization developmental cell growth growth developmental growth involved in morphogenesis generation of neurons anatomical structure morphogenesis neuron development actin cytoskeleton organization postsynapse organization postsynaptic cytoskeleton organization organelle organization cell junction organization postsynaptic actin cytoskeleton organization actin filament-based process synapse organization cytoskeleton organization cellular response to endogenous stimulus cellular response to growth factor stimulus response to stimulus response to endogenous stimulus cellular response to nerve growth factor stimulus cellular response to brain-derived neurotrophic factor stimulus response to nerve growth factor response to growth factor cellular response to stimulus regulation of cellular process signaling negative regulation of signaling negative regulation of ERBB signaling pathway negative regulation of biological process regulation of signal transduction cell surface receptor protein tyrosine kinase signaling pathway negative regulation of cell communication cell communication regulation of epidermal growth factor receptor signaling pathway negative regulation of cellular process epidermal growth factor receptor signaling pathway signal transduction enzyme-linked receptor protein signaling pathway regulation of biological process regulation of signaling regulation of ERBB signaling pathway cell surface receptor signaling pathway negative regulation of response to stimulus biological regulation negative regulation of signal transduction regulation of response to stimulus negative regulation of epidermal growth factor receptor signaling pathway ERBB signaling pathway regulation of cell communication regulation of localization regulation of cellular component organization receptor internalization regulation of transport regulation of receptor-mediated endocytosis regulation of vesicle-mediated transport regulation of receptor internalization receptor-mediated endocytosis regulation of endocytosis negative regulation of intracellular signal transduction intracellular signal transduction regulation of intracellular signal transduction intracellular signaling cassette regulation of MAPK cascade MAPK cascade negative regulation of MAPK cascade regulation of blood-brain barrier permeability system process maintenance of blood-brain barrier homeostatic process tissue homeostasis regulation of vascular permeability negative regulation of vascular permeability circulatory system process multicellular organismal-level homeostasis vascular process in circulatory system anatomical structure homeostasis regulation of biological quality blood circulation negative regulation of blood-brain barrier permeability regulation of biosynthetic process negative regulation of metabolic process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulation of gene expression negative regulation of gene expression biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process regulation of macromolecule biosynthetic process metabolic process macromolecule metabolic process regulation of metabolic process negative regulation of macromolecule metabolic process	membrane-bounded organelle intracellular anatomical structure intracellular vesicle intracellular organelle cellular anatomical structure bounding membrane of organelle cytoplasmic vesicle vesicle membrane clathrin-coated vesicle endocytic vesicle membrane coated vesicle vesicle endocytic vesicle clathrin-coated vesicle membrane membrane-bounded organelle intracellular anatomical structure intracellular vesicle intracellular organelle cellular anatomical structure bounding membrane of organelle cytoplasmic vesicle vesicle membrane clathrin-coated vesicle endocytic vesicle membrane coated vesicle vesicle endocytic vesicle clathrin-coated vesicle membrane clathrin-coated endocytic vesicle membrane membrane intracellular membrane-bounded organelle clathrin-coated endocytic vesicle cytoplasmic vesicle membrane coated vesicle membrane organelle cytoplasm organelle membrane cytosol presynapse presynaptic cytosol synapse cell junction cell periphery plasma membrane glutamatergic synapse early endosome endosome endomembrane system photoreceptor ribbon synapse ribbon synapse Golgi membrane Golgi apparatus perinuclear region of cytoplasm postsynapse

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR004148	BAR domain	Domain
A	IPR050384	Endophilin/SH3RF	Family
A	IPR036028	SH3-like domain superfamily	Homologous Superfamily
A	IPR027267	AH/BAR domain superfamily	Homologous Superfamily
A	IPR001452	SH3 domain	Domain
A	IPR035824	Endophilin-A, SH3 domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	Pharos: Q99962	astrocytic tumor glioblastoma lung carcinoma medulloblastoma ovarian cancer primitive neuroectodermal tumor transitional cell carcinoma atypical teratoid rhabdoid tumor interstitial cystitis malignant ependymoma nephrosclerosis Pick disease psoriasis gastric carcinoma large cell medulloblastoma astrocytic tumor glioblastoma lung carcinoma medulloblastoma ovarian cancer primitive neuroectodermal tumor transitional cell carcinoma atypical teratoid rhabdoid tumor interstitial cystitis malignant ependymoma nephrosclerosis Pick disease psoriasis gastric carcinoma large cell medulloblastoma malignant glioma oligodendroglioma pilocytic astrocytoma subependymal giant cell astrocytoma

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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.