1GZS

CRYSTAL STRUCTURE OF THE COMPLEX BETWEEN THE GEF DOMAIN OF THE SALMONELLA TYPHIMURIUM SOPE TOXIN AND HUMAN Cdc42

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	d1gzsa_	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	G proteins	CDC42	(Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d1gzsc_	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	G proteins	CDC42	(Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d1gzsb_	All alpha proteins	SopE-like GEF domain	SopE-like GEF domain	SopE-like GEF domain	GEF domain of SopE toxin	(Salmonella enterica subsp. enterica serovar Typhimurium ) [TaxId: 90371 ],	SCOPe (2.08)
D	d1gzsd_	All alpha proteins	SopE-like GEF domain	SopE-like GEF domain	SopE-like GEF domain	GEF domain of SopE toxin	(Salmonella enterica subsp. enterica serovar Typhimurium ) [TaxId: 90371 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Ras-like P-loop GTPases	8057416	3002022	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Ras-like P-loop GTPases	8057416	3002022	SCOP2B (2022-06-29)
B	SCOP2 Family	SopE-like GEF domain	8029940	4002417	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	SopE-like GEF domain	8042319	3001205	SCOP2 (2022-06-29)
D	SCOP2B Superfamily	SopE-like GEF domain	8042319	3001205	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	Ras	e1gzsA1	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)
C	Ras	e1gzsC1	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)
B	SopE_GEF	e1gzsB1	A: alpha arrays	X: SopE-like GEF domain (From Topology)	H: SopE-like GEF domain (From Topology)	T: SopE-like GEF domain	F: SopE_GEF	ECOD (1.6)
D	SopE_GEF	e1gzsD1	A: alpha arrays	X: SopE-like GEF domain (From Topology)	H: SopE-like GEF domain (From Topology)	T: SopE-like GEF domain	F: SopE_GEF	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
C	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
B	1.10.4120.10	Mainly Alpha	Orthogonal Bundle	SopE-like GEF fold	SopE-like, GEF domain	CATH (4.3.0)
D	1.10.4120.10	Mainly Alpha	Orthogonal Bundle	SopE-like GEF fold	SopE-like, GEF domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, C	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, motil ...	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
B, D	PF07487	SopE GEF domain (SopE_GEF)	SopE GEF domain	This family represents the C-terminal guanine nucleotide exchange factor (GEF) domain of SopE. Salmonella typhimurium employs a type III secretion system to inject bacterial toxins into the host cell cytosol. These toxins transiently activate Rho fam ...	This family represents the C-terminal guanine nucleotide exchange factor (GEF) domain of SopE. Salmonella typhimurium employs a type III secretion system to inject bacterial toxins into the host cell cytosol. These toxins transiently activate Rho family GTP-binding protein-dependent signaling cascades to induce cytoskeletal rearrangements. SopE, can activate Cdc42, an essential component of the host cellular signaling cascade, in a Dbl-like fashion despite its lack of sequence similarity to Dbl-like proteins, the Rho-specific eukaryotic guanine nucleotide exchange factors [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, C	GTP-BINDING PROTEIN	protein binding binding protein domain specific binding GBD domain binding thioesterase binding enzyme binding pyrophosphatase activity GTPase activity ribonucleoside triphosphate phosphatase activity hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides hydrolase activity hydrolase activity, acting on acid anhydrides catalytic activity GTP-dependent protein binding protein binding binding protein domain specific binding GBD domain binding thioesterase binding enzyme binding pyrophosphatase activity GTPase activity ribonucleoside triphosphate phosphatase activity hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides hydrolase activity hydrolase activity, acting on acid anhydrides catalytic activity GTP-dependent protein binding guanyl nucleotide binding GTP binding nucleotide binding guanyl ribonucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding organic cyclic compound binding purine nucleotide binding anion binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding kinase binding protein kinase binding aminoacyltransferase activity ubiquitin-like protein transferase activity catalytic activity, acting on a protein acyltransferase activity ubiquitin-like protein ligase activity ubiquitin protein ligase activity transferase activity ubiquitin-protein transferase activity signaling receptor binding apolipoprotein A-I receptor binding apolipoprotein receptor binding mitogen-activated protein kinase kinase kinase binding identical protein binding G protein activity molecular function regulator activity	regulation of cytokinesis regulation of biological process regulation of cellular process positive regulation of cell division regulation of cell cycle process biological regulation positive regulation of biological process cytokinesis positive regulation of cell cycle regulation of cell division positive regulation of cytokinesis positive regulation of cell cycle process cellular process cell division regulation of cytokinesis regulation of biological process regulation of cellular process positive regulation of cell division regulation of cell cycle process biological regulation positive regulation of biological process cytokinesis positive regulation of cell cycle regulation of cell division positive regulation of cytokinesis positive regulation of cell cycle process cellular process cell division cell cycle regulation of cell cycle positive regulation of cellular process cell cycle process protein localization localization cellular localization cellular macromolecule localization macromolecule localization regulation of cellular component organization positive regulation of cellular component organization cell projection organization plasma membrane bounded cell projection assembly cellular component biogenesis cellular component organization pseudopodium assembly cellular component assembly positive regulation of cell projection organization cellular component organization or biogenesis plasma membrane bounded cell projection organization positive regulation of cellular component biogenesis regulation of cell projection organization regulation of cell projection assembly regulation of cellular component biogenesis regulation of plasma membrane bounded cell projection assembly positive regulation of pseudopodium assembly regulation of pseudopodium assembly cell projection assembly regulation of plasma membrane bounded cell projection organization positive regulation of plasma membrane bounded cell projection assembly pseudopodium organization establishment of organelle localization transport nucleus localization intracellular transport establishment of localization organelle localization establishment of localization in cell nuclear migration positive regulation of substrate adhesion-dependent cell spreading regulation of cell-substrate adhesion positive regulation of cell adhesion regulation of substrate adhesion-dependent cell spreading regulation of cell adhesion cell-substrate adhesion cell adhesion positive regulation of cell-substrate adhesion substrate adhesion-dependent cell spreading cellular response to stimulus cell surface receptor signaling pathway response to stimulus neuropilin signaling pathway signaling cell communication signal transduction multicellular organismal process cellular developmental process plasma membrane bounded cell projection morphogenesis cell development neuron projection development cell morphogenesis neurogenesis multicellular organism development cell projection morphogenesis neuron differentiation neuron projection morphogenesis dendrite development cell differentiation anatomical structure development dendritic spine morphogenesis synapse organization system development developmental process dendritic spine development dendritic spine organization postsynapse organization dendrite morphogenesis nervous system development cell morphogenesis involved in neuron differentiation generation of neurons anatomical structure morphogenesis cell junction organization neuron development neuron projection organization gland development animal organ development salivary gland development gland morphogenesis salivary gland morphogenesis anatomical structure formation involved in morphogenesis animal organ morphogenesis exocrine system development submandibular salivary gland formation organelle organization actin cytoskeleton organization actin filament organization actin filament-based process supramolecular fiber organization cytoskeleton organization regulation of postsynapse organization regulation of synapse organization regulation of synapse structure or activity regulation of biological quality attachment of spindle microtubules to kinetochore metaphase chromosome alignment chromosome localization nuclear chromosome segregation regulation of attachment of spindle microtubules to kinetochore establishment of chromosome localization chromosome segregation organelle transport along microtubule microtubule-based transport transport along microtubule cytoskeleton-dependent intracellular transport microtubule-based movement microtubule-based process Golgi localization establishment of Golgi localization regulation of growth growth positive regulation of cell growth regulation of cell growth cell growth positive regulation of growth positive regulation of cell population proliferation respiratory tube development epithelial cell proliferation involved in lung morphogenesis lung development respiratory system development lung morphogenesis epithelial cell proliferation regulation of epithelial cell proliferation involved in lung morphogenesis epithelium development cell population proliferation positive regulation of epithelial cell proliferation involved in lung morphogenesis tube development positive regulation of epithelial cell proliferation lung epithelium development tissue development regulation of cell population proliferation regulation of epithelial cell proliferation regulation of cytoskeleton organization regulation of actin filament-based process regulation of organelle organization regulation of actin cytoskeleton organization regulation of synapse structural plasticity positive regulation of synapse structural plasticity polarized epithelial cell differentiation establishment of monopolar cell polarity establishment or maintenance of monopolar cell polarity establishment or maintenance of cell polarity epithelial cell differentiation morphogenesis of a polarized epithelium establishment or maintenance of apical/basal cell polarity establishment or maintenance of bipolar cell polarity establishment of epithelial cell apical/basal polarity morphogenesis of an epithelium establishment of cell polarity tissue morphogenesis establishment or maintenance of epithelial cell apical/basal polarity establishment of apical/basal cell polarity establishment of epithelial cell polarity heart process system process circulatory system process heart contraction blood circulation biological process involved in interspecies interaction between organisms immune response response to other organism defense response response to type II interferon response to cytokine defense response to symbiont response to external stimulus cellular response to type II interferon response to biotic stimulus response to peptide response to chemical immune system process defense response to other organism response to stress innate immune response cellular response to cytokine stimulus response to external biotic stimulus head development brain development substantia nigra development central nervous system development midbrain development neural nucleus development myeloid leukocyte differentiation hemopoiesis macrophage differentiation mononuclear cell differentiation myeloid cell differentiation leukocyte differentiation positive regulation of locomotion regulation of cell motility positive regulation of cell migration regulation of locomotion positive regulation of cell motility regulation of cell migration cell migration cell motility locomotion filopodium assembly regulation of filopodium assembly positive regulation of filopodium assembly modification of synaptic structure regulation of lamellipodium assembly regulation of lamellipodium organization lamellipodium assembly positive regulation of lamellipodium assembly positive regulation of lamellipodium organization lamellipodium organization positive regulation of organelle organization regulation of actin filament bundle assembly positive regulation of actin filament bundle assembly actin filament bundle organization positive regulation of stress fiber assembly stress fiber assembly regulation of actin filament organization actomyosin structure organization positive regulation of cytoskeleton organization positive regulation of supramolecular fiber organization regulation of stress fiber assembly contractile actin filament bundle assembly regulation of actomyosin structure organization actin filament bundle assembly regulation of supramolecular fiber organization endothelin receptor signaling pathway involved in heart process endothelin receptor signaling pathway G protein-coupled receptor signaling pathway G protein-coupled receptor signaling pathway involved in heart process Golgi organization endomembrane system organization adherens junction organization cell-cell junction organization membrane organization import into cell vesicle-mediated transport phagocytosis, engulfment membrane invagination phagocytosis endocytosis plasma membrane invagination actin filament branching dendritic cell migration leukocyte migration mononuclear cell migration positive regulation of nucleobase-containing compound metabolic process positive regulation of DNA replication primary metabolic process DNA metabolic process regulation of macromolecule metabolic process nucleic acid metabolic process regulation of primary metabolic process nucleobase-containing compound metabolic process positive regulation of metabolic process DNA replication positive regulation of DNA metabolic process metabolic process positive regulation of macromolecule metabolic process macromolecule metabolic process regulation of nucleobase-containing compound metabolic process regulation of metabolic process regulation of DNA metabolic process regulation of DNA replication neuron apoptotic process positive regulation of programmed cell death regulation of apoptotic process regulation of programmed cell death cell death positive regulation of apoptotic process apoptotic process positive regulation of neuron apoptotic process programmed cell death regulation of neuron apoptotic process negative regulation of cellular component organization protein-containing complex organization negative regulation of biological process negative regulation of protein-containing complex assembly regulation of protein-containing complex assembly protein-containing complex assembly negative regulation of cellular process blood vessel morphogenesis angiogenesis sprouting angiogenesis vasculature development circulatory system development tube morphogenesis blood vessel development neuron fate commitment cell fate determination neuron fate determination cell fate commitment positive regulation of cell communication positive regulation of signal transduction regulation of signal transduction intracellular signal transduction positive regulation of response to stimulus positive regulation of JNK cascade regulation of intracellular signal transduction JNK cascade intracellular signaling cassette regulation of signaling positive regulation of MAPK cascade regulation of JNK cascade positive regulation of intracellular signal transduction regulation of MAPK cascade regulation of response to stimulus MAPK cascade regulation of cell communication positive regulation of signaling Wnt signaling pathway, planar cell polarity pathway non-canonical Wnt signaling pathway Wnt signaling pathway cell junction assembly mitotic nuclear division organelle fission regulation of mitotic nuclear division mitotic cell cycle regulation of mitotic cell cycle nuclear division mitotic cell cycle process regulation of nuclear division small GTPase-mediated signal transduction Cdc42 protein signal transduction Rho protein signal transduction regulation of localization establishment of protein localization nitrogen compound transport regulation of protein localization positive regulation of establishment of protein localization positive regulation of protein transport positive regulation of intracellular transport regulation of intracellular transport regulation of transport regulation of establishment of protein localization regulation of protein transport positive regulation of transport protein transport regulation of cellular localization positive regulation of protein localization regulation of intracellular protein transport positive regulation of intracellular protein transport intracellular protein transport regulation of modification of synaptic structure regulation of modification of postsynaptic structure modification of postsynaptic structure integrin-mediated signaling pathway modulation by host of viral process modulation by host of symbiont process biological process involved in interaction with symbiont biological process involved in symbiotic interaction heart development embryo development embryonic heart tube development embryonic organ development regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction phosphatidylinositol 3-kinase/protein kinase B signal transduction positive regulation of endocytosis regulation of endocytosis positive regulation of pinocytosis regulation of vesicle-mediated transport regulation of pinocytosis pinocytosis cardiac conduction system development cardiac muscle tissue development striated muscle tissue development muscle tissue development heart morphogenesis cardiac neural crest cell development involved in heart development neural crest cell development mesenchyme development mesenchymal cell migration ameboidal-type cell migration neural crest cell migration stem cell development cardiac neural crest cell development involved in outflow tract morphogenesis neural crest cell differentiation cell migration involved in heart development cardiocyte differentiation stem cell differentiation cardiac neural crest cell differentiation involved in heart development outflow tract morphogenesis mesenchymal cell differentiation cardiac neural crest cell migration involved in outflow tract morphogenesis	cell-cell junction anchoring junction cell junction cellular anatomical entity intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle Golgi membrane Golgi apparatus membrane intracellular membrane-bounded organelle endomembrane system intracellular organelle cell-cell junction anchoring junction cell junction cellular anatomical entity intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle Golgi membrane Golgi apparatus membrane intracellular membrane-bounded organelle endomembrane system intracellular organelle bounding membrane of organelle organelle organelle membrane neuron spine synapse neuron projection dendritic spine plasma membrane bounded cell projection somatodendritic compartment cell projection postsynapse dendrite dendritic tree midbody focal adhesion cell-substrate junction intracellular vesicle phagocytic vesicle cytoplasmic vesicle vesicle endocytic vesicle cell periphery plasma membrane protein-containing complex organelle subcompartment endoplasmic reticulum subcompartment nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum endoplasmic reticulum membrane intracellular non-membrane-bounded organelle cytoplasmic ribonucleoprotein granule supramolecular complex non-membrane-bounded organelle ribonucleoprotein granule Schaffer collateral - CA1 synapse cell leading edge leading edge membrane apical part of cell cytoskeleton spindle spindle midzone microtubule cytoskeleton extracellular exosome extracellular vesicle extracellular organelle extracellular region extracellular space extracellular membrane-bounded organelle secretory granule secretory vesicle glutamatergic synapse Golgi transport complex vesicle tethering complex storage vacuole vacuole cell body neuronal cell body actin-based cell projection filopodium centrosome microtubule organizing center mitotic spindle
B, D	SOPE	GTPase regulator activity enzyme regulator activity enzyme activator activity GTPase activator activity molecular function activator activity nucleoside-triphosphatase regulator activity molecular function regulator activity guanyl-nucleotide exchange factor activity	cellular component organization organelle organization actin cytoskeleton organization actin filament-based process cellular process cellular component organization or biogenesis cytoskeleton organization	extracellular region cellular anatomical entity

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, C	IPR001806	Small GTPase	Family
A, C	IPR003578	Small GTPase Rho	Family
A, C	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
A, C	IPR037874	Cdc42	Family
A, C	IPR005225	Small GTP-binding domain	Domain
B, D	IPR005414	Guanine nucleotide exchange factor SopE	Family
B, D	IPR016019	Guanine nucleotide exchange factor SopE, GEF domain	Domain
B, D	IPR016018	Guanine nucleotide exchange factor SopE, N-terminal domain	Domain
B, D	IPR035949	SopE-like, GEF domain superfamily	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, C	Pharos: P60953	macrothrombocytopenia-lymphedema-developmental delay-facial dysmorphism-camptodactyly syndrome Necrosis sarcomatoid carcinoma carcinoma intellectual disability HIV infectious disease lung cancer malignant ependymoma mammary neoplasms, animal Pick disease atrial fibrillation undifferentiated carcinoma gastric cancer hepatocellular carcinoma lymphatic system disease macrothrombocytopenia-lymphedema-developmental delay-facial dysmorphism-camptodactyly syndrome Necrosis sarcomatoid carcinoma carcinoma intellectual disability HIV infectious disease lung cancer malignant ependymoma mammary neoplasms, animal Pick disease atrial fibrillation undifferentiated carcinoma gastric cancer hepatocellular carcinoma lymphatic system disease malignant glioma oligodendroglioma adrenal gland cancer pilocytic astrocytoma schizophrenia atypical teratoid rhabdoid tumor uterine corpus leiomyoma gastric carcinoma large cell medulloblastoma medulloblastoma ovarian cancer plasma cell myeloma astrocytic tumor subependymal giant cell astrocytoma cancer endometriosis glioblastoma

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.