7C7I | pdb_00007c7i

Crystal structure of SHANK3 SPN domain in complex with GTP-bound Rap1b(E30D,K31E)

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)
B	d7c7ib_	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	G proteins	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d7c7ia_	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	G proteins	automated matches	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)
B	SCOP2B Superfamily	Ras-like P-loop GTPases	8057488	3002022	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Ras-like P-loop GTPases	8057488	3002022	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)
D	FERM_f0	e7c7iD1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: FERM_f0	ECOD (1.6)
C	FERM_f0	e7c7iC1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: FERM_f0	ECOD (1.6)
B	Ras	e7c7iB1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Ras	ECOD (1.6)
A	Ras	e7c7iA1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Ras	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	3.10.20.90	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Phosphatidylinositol 3-kinase Catalytic Subunit	CATH (utative)
C	3.10.20.90	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Phosphatidylinositol 3-kinase Catalytic Subunit	CATH (utative)
B	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (utative)
A	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (utative)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
C, D	PF12796	Ankyrin repeats (3 copies) (Ank_2)	Ankyrin repeats (3 copies)	-	Repeat
A, B	PF00071	Ras family (Ras)	Ras family	Includes sub-families Ras, Rab, Rac, Ral, Ran, Rap Ypt1 and more. Shares P-loop motif with GTP_EFTU, arf and myosin_head. See Pfam:PF00009 Pfam:PF00025, Pfam:PF00063. As regards Rab GTPases, these are important regulators of vesicle formation, motili ...	Includes sub-families Ras, Rab, Rac, Ral, Ran, Rap Ypt1 and more. Shares P-loop motif with GTP_EFTU, arf and myosin_head. See Pfam:PF00009 Pfam:PF00025, Pfam:PF00063. As regards Rab GTPases, these are important regulators of vesicle formation, motility and fusion. They share a fold in common with all Ras GTPases: this is a six-stranded beta-sheet surrounded by five alpha-helices [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C, D	SH3 and multiple ankyrin repeat domains protein 3	SH3 domain binding protein binding binding protein domain specific binding signaling receptor complex adaptor activity protein-macromolecule adaptor activity synaptic receptor adaptor activity molecular adaptor activity signaling adaptor activity scaffold protein binding ionotropic glutamate receptor binding signaling receptor binding glutamate receptor binding cytoskeletal protein binding SH3 domain binding protein binding binding protein domain specific binding signaling receptor complex adaptor activity protein-macromolecule adaptor activity synaptic receptor adaptor activity molecular adaptor activity signaling adaptor activity scaffold protein binding ionotropic glutamate receptor binding signaling receptor binding glutamate receptor binding cytoskeletal protein binding actin binding cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding	cellular response to stimulus positive regulation of cell communication multicellular organismal process regulation of postsynaptic membrane potential system process regulation of cellular process positive regulation of signal transduction response to stimulus signaling modulation of chemical synaptic transmission regulation of system process positive regulation of excitatory postsynaptic potential positive regulation of biological process regulation of signal transduction chemical synaptic transmission, postsynaptic cellular response to stimulus positive regulation of cell communication multicellular organismal process regulation of postsynaptic membrane potential system process regulation of cellular process positive regulation of signal transduction response to stimulus signaling modulation of chemical synaptic transmission regulation of system process positive regulation of excitatory postsynaptic potential positive regulation of biological process regulation of signal transduction chemical synaptic transmission, postsynaptic cell communication positive regulation of response to stimulus synaptic signaling modulation of excitatory postsynaptic potential regulation of multicellular organismal process signal transduction regulation of biological quality positive regulation of cellular process trans-synaptic signaling regulation of biological process regulation of signaling cell surface receptor signaling pathway nervous system process biological regulation cell-cell signaling chemical synaptic transmission regulation of nervous system process regulation of trans-synaptic signaling regulation of response to stimulus anterograde trans-synaptic signaling regulation of cell communication cellular process excitatory postsynaptic potential regulation of membrane potential positive regulation of signaling membrane organization cellular localization postsynapse organization AMPA glutamate receptor clustering glutamate receptor clustering neurotransmitter-gated ion channel clustering localization within membrane protein localization to membrane cellular component organization localization cell junction organization receptor clustering macromolecule localization cellular component organization or biogenesis synapse organization intracellular protein localization postsynaptic membrane organization behavior learning learning or memory cognition imitative learning auditory behavior vocal learning learned vocalization behavior or vocal learning response to mechanical stimulus response to external stimulus mechanosensory behavior response to auditory stimulus observational learning response to abiotic stimulus long-term synaptic potentiation regulation of synaptic plasticity positive regulation of synaptic transmission regulation of long-term synaptic potentiation regulation of cytoskeleton organization regulation of cellular component organization regulation of actin filament-based process negative regulation of biological process regulation of actin filament bundle assembly cellular component biogenesis cellular component assembly actin filament bundle organization negative regulation of cellular process actin filament-based process negative regulation of supramolecular fiber organization regulation of actin filament organization negative regulation of cellular component organization actin cytoskeleton organization negative regulation of cytoskeleton organization actin filament organization negative regulation of actin filament bundle assembly regulation of cellular component biogenesis regulation of organelle organization organelle organization negative regulation of organelle organization regulation of actin cytoskeleton organization actin filament bundle assembly regulation of supramolecular fiber organization supramolecular fiber organization cytoskeleton organization memory regulation of developmental process cellular developmental process cell projection organization positive regulation of dendritic spine development cell development regulation of dendritic spine development neuron projection development positive regulation of developmental process neurogenesis multicellular organism development neuron differentiation dendrite development cell differentiation anatomical structure development system development developmental process dendritic spine development plasma membrane bounded cell projection organization nervous system development generation of neurons neuron development regulation of cellular component size homeostatic process cell volume homeostasis negative regulation of cell volume cellular homeostasis regulation of cell size regulation of anatomical structure size intracellular signal transduction intracellular signaling cassette MAPK cascade plasma membrane bounded cell projection morphogenesis cell morphogenesis cell projection morphogenesis neuron projection morphogenesis dendritic spine morphogenesis dendritic spine organization dendrite morphogenesis cell morphogenesis involved in neuron differentiation anatomical structure morphogenesis neuron projection organization NMDA glutamate receptor clustering guanylate kinase-associated protein clustering cell junction assembly synapse assembly forebrain development central nervous system neuron differentiation GABAergic neuron differentiation striatum development subpallium development striatal medium spiny neuron differentiation head development forebrain generation of neurons animal organ development brain development central nervous system development telencephalon development forebrain neuron differentiation regulation of synapse structure or activity regulation of cell projection organization regulation of postsynapse organization regulation of neuron projection development regulation of anatomical structure morphogenesis regulation of synapse organization regulation of dendritic spine morphogenesis regulation of plasma membrane bounded cell projection organization positive regulation of long-term synaptic potentiation synaptic transmission, glutamatergic regulation of synaptic transmission, glutamatergic positive regulation of synaptic transmission, glutamatergic brain morphogenesis animal organ morphogenesis adult behavior positive regulation of cellular component organization regulation of synapse structural plasticity positive regulation of synapse structural plasticity postsynaptic density organization organelle assembly postsynaptic specialization assembly postsynapse assembly excitatory synapse assembly postsynaptic specialization organization postsynaptic density assembly neuromuscular process neuromuscular process controlling balance glutamate receptor signaling pathway positive regulation of glutamate receptor signaling pathway regulation of glutamate receptor signaling pathway biological process involved in intraspecies interaction between organisms social behavior negative regulation of signaling negative regulation of synaptic transmission negative regulation of cell communication long-term synaptic depression regulation of long-term synaptic depression positive regulation of nervous system development regulation of long-term neuronal synaptic plasticity regulation of cell differentiation regulation of neurogenesis regulation of cell development regulation of nervous system development positive regulation of cell differentiation positive regulation of long-term neuronal synaptic plasticity positive regulation of neurogenesis regulation of neuronal synaptic plasticity regulation of multicellular organismal development positive regulation of cell development positive regulation of multicellular organismal process vocalization behavior	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol cell projection neuron projection plasma membrane bounded cell projection neuron spine synapse dendritic spine somatodendritic compartment postsynapse cell junction dendrite cellular anatomical structure intracellular anatomical structure cytoplasm cytosol cell projection neuron projection plasma membrane bounded cell projection neuron spine synapse dendritic spine somatodendritic compartment postsynapse cell junction dendrite dendritic tree cell periphery plasma membrane membrane membrane-bounded organelle cilium ciliary membrane bounding membrane of organelle organelle plasma membrane region organelle membrane cell projection membrane postsynaptic density neuron to neuron synapse postsynaptic specialization asymmetric synapse
A, B	Ras-related protein Rap-1b	binding guanyl nucleotide binding GTP binding nucleotide binding guanyl ribonucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding binding guanyl nucleotide binding GTP binding nucleotide binding guanyl ribonucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding GDP binding protein-containing complex binding pyrophosphatase activity GTPase activity G protein activity ribonucleoside triphosphate phosphatase activity molecular function regulator activity hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides hydrolase activity hydrolase activity, acting on acid anhydrides catalytic activity	cellular component organization cell junction organization cellular process synapse organization cellular component organization or biogenesis modification of postsynaptic structure modification of synaptic structure regulation of localization regulated exocytosis regulation of cellular process synaptic vesicle cycle negative regulation of biological process synaptic vesicle exocytosis negative regulation of transport cellular component organization cell junction organization cellular process synapse organization cellular component organization or biogenesis modification of postsynaptic structure modification of synaptic structure regulation of localization regulated exocytosis regulation of cellular process synaptic vesicle cycle negative regulation of biological process synaptic vesicle exocytosis negative regulation of transport vesicle-mediated transport cell communication vesicle-mediated transport in synapse localization negative regulation of secretion establishment of localization in cell negative regulation of secretion by cell trans-synaptic signaling regulation of biological process neurotransmitter secretion regulation of synaptic vesicle exocytosis neurotransmitter transport establishment of localization negative regulation of synaptic vesicle exocytosis regulation of secretion signal release from synapse regulation of trans-synaptic signaling exocytosis cellular localization transport modulation of chemical synaptic transmission signaling negative regulation of regulated secretory pathway regulation of regulated secretory pathway synaptic signaling regulation of secretion by cell secretion by cell negative regulation of exocytosis signal release negative regulation of cellular process regulation of signaling regulation of transport secretion regulation of neurotransmitter transport biological regulation export from cell cell-cell signaling regulation of vesicle-mediated transport chemical synaptic transmission regulation of neurotransmitter secretion anterograde trans-synaptic signaling regulation of exocytosis regulation of cell communication cellular response to stimulus small GTPase-mediated signal transduction response to stimulus intracellular signal transduction intracellular signaling cassette signal transduction Rap protein signal transduction calcium-ion regulated exocytosis positive regulation of cell communication positive regulation of signal transduction positive regulation of biological process regulation of signal transduction positive regulation of response to stimulus positive regulation of ERK1 and ERK2 cascade regulation of intracellular signal transduction positive regulation of cellular process positive regulation of MAPK cascade positive regulation of intracellular signal transduction regulation of MAPK cascade regulation of response to stimulus MAPK cascade ERK1 and ERK2 cascade regulation of ERK1 and ERK2 cascade positive regulation of signaling cell population proliferation cellular response to nitrogen compound response to organophosphorus response to oxygen-containing compound response to nitrogen compound response to purine-containing compound response to cAMP cellular response to oxygen-containing compound cellular response to chemical stimulus response to chemical cellular response to cAMP regulation of calcium ion-dependent exocytosis negative regulation of calcium ion-dependent exocytosis positive regulation of cellular component organization regulation of cellular component organization protein-containing complex organization positive regulation of cellular component biogenesis regulation of cellular component biogenesis cellular component biogenesis positive regulation of protein-containing complex assembly regulation of protein-containing complex assembly cellular component assembly protein-containing complex assembly regulation of integrin activation integrin activation positive regulation of integrin activation regulation of cell junction assembly cell junction assembly developmental process epithelium development endothelial cell differentiation cellular developmental process endothelium development cell development tissue development epithelial cell differentiation endothelial cell development epithelial cell development cell differentiation establishment of endothelial barrier anatomical structure development regulation of establishment of cell polarity regulation of establishment or maintenance of cell polarity establishment of cell polarity establishment or maintenance of cell polarity	cellular anatomical structure membrane cell-cell junction anchoring junction cell junction extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle extracellular space vesicle extracellular membrane-bounded organelle cellular anatomical structure membrane cell-cell junction anchoring junction cell junction extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle extracellular space vesicle extracellular membrane-bounded organelle intracellular anatomical structure intracellular vesicle lytic vacuole endomembrane system intracellular organelle bounding membrane of organelle vesicle membrane cytoplasmic vesicle lysosome vacuolar membrane azurophil granule vacuole intracellular membrane-bounded organelle lytic vacuole membrane cytoplasmic vesicle membrane lysosomal membrane secretory granule primary lysosome secretory vesicle azurophil granule membrane cytoplasm organelle membrane secretory granule membrane cytosol cell periphery plasma membrane synapse glutamatergic synapse lipid droplet membraneless organelle intracellular membraneless organelle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C, D	IPR036028	SH3-like domain superfamily	Homologous Superfamily
C, D	IPR002110	Ankyrin repeat	Repeat
C, D	IPR001452	SH3 domain	Domain
C, D	IPR051569	SH3 and multiple ankyrin repeat domains protein	Family
C, D	IPR001660	Sterile alpha motif domain	Domain
C, D	IPR036770	Ankyrin repeat-containing domain superfamily	Homologous Superfamily
C, D	IPR013761	Sterile alpha motif/pointed domain superfamily	Homologous Superfamily
C, D	IPR041489	PDZ domain 6	Domain
C, D	IPR036034	PDZ superfamily	Homologous Superfamily
C, D	IPR001478	PDZ domain	Domain
A, B	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
A, B	IPR005225	Small GTP-binding domain	Domain
A, B	IPR020849	Small GTPase, Ras-type	Family
A, B	IPR001806	Small GTPase	Family
A, B	IPR038851	Ras-related protein Rap1	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
C, D	Pharos: Q9BYB0	Phelan-McDermid syndrome intellectual disability schizophrenia 15 autism schizophrenia autism spectrum disorder Language Development Disorders large cell medulloblastoma malignant glioma medulloblastoma non-small cell lung carcinoma astrocytic tumor pancreatic intraductal papillary-mucinous neoplasm pilocytic astrocytoma developmental disability Phelan-McDermid syndrome intellectual disability schizophrenia 15 autism schizophrenia autism spectrum disorder Language Development Disorders large cell medulloblastoma malignant glioma medulloblastoma non-small cell lung carcinoma astrocytic tumor pancreatic intraductal papillary-mucinous neoplasm pilocytic astrocytoma developmental disability lung adenocarcinoma oligodendroglioma atypical teratoid rhabdoid tumor pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia primitive neuroectodermal tumor breast carcinoma subependymal giant cell astrocytoma ductal breast carcinoma in situ interstitial cystitis malignant ependymoma pancreatic intraductal papillary-mucinous carcinoma auditory perceptual disorders breast fibroadenoma glioblastoma invasive ductal breast carcinoma
A, B	Pharos: P61224	Kabuki syndrome lung adenocarcinoma

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.