4FME | pdb_00004fme

EspG-Rab1-Arf6 complex

External Resource: Annotation

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

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	8057282	3002022	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Ras-like P-loop GTPases	8057282	3002022	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Ras-like P-loop GTPases	8057436	3002022	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Ras-like P-loop GTPases	8057436	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)
B	RRM_1	e4fmeB1	A: alpha bundles	X: beta-Grasp	H: HTH	T: winged helix domain	F: RRM_1	ECOD (develop294)
E	RRM_1	e4fmeE1	A: alpha bundles	X: beta-Grasp	H: HTH	T: winged helix domain	F: RRM_1	ECOD (develop294)
C	Cytochrom_C	e4fmeC1	A: alpha bundles	X: Flavodoxin-like	H: Precorrin-8X methylmutase CbiC/CobH	T: Precorrin-8X methylmutase CbiC/CobH	F: Cytochrom_C	ECOD (develop294)
F	ABC_tran	e4fmeF1	A: alpha bundles	X: beta-Grasp	H: HTH	T: winged helix domain	F: ABC_tran	ECOD (develop294)
D	AAA_2	e4fmeD1	A: alpha bundles	X: TIM beta/alpha-barrel	H: TIM barrels	T: TIM barrels	F: AAA_2	ECOD (develop294)
A	AAA_2	e4fmeA1	A: alpha bundles	X: TIM beta/alpha-barrel	H: TIM barrels	T: TIM barrels	F: AAA_2	ECOD (develop294)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B, E	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
C, F	PF00025	ADP-ribosylation factor family (Arf)	ADP-ribosylation factor family	Pfam combines a number of different Prosite families together	Domain
A, D	PF06872	EspG protein (EspG)	EspG protein	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B, E	Ras-related protein Rab-1A	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 cell adhesion molecule binding cadherin binding protein 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 cation binding metal ion binding	virion assembly viral process viral life cycle autophagosome assembly catabolic process organelle assembly vacuole organization macroautophagy autophagy autophagosome organization cellular component biogenesis cellular component organization organelle organization cellular component assembly virion assembly viral process viral life cycle autophagosome assembly catabolic process organelle assembly vacuole organization macroautophagy autophagy autophagosome organization cellular component biogenesis cellular component organization organelle organization cellular component assembly cellular process metabolic process cellular component organization or biogenesis process utilizing autophagic mechanism regulation of biological process regulation of cellular process positive regulation of glycoprotein metabolic process positive regulation of protein metabolic process regulation of protein metabolic process biological regulation positive regulation of biological process carbohydrate derivative metabolic process primary metabolic process regulation of macromolecule metabolic process glycoprotein metabolic process regulation of primary metabolic process regulation of glycoprotein metabolic process positive regulation of metabolic process positive regulation of macromolecule metabolic process protein metabolic process macromolecule metabolic process regulation of metabolic process positive regulation of cellular process establishment of organelle localization vesicle cytoskeletal trafficking vesicle localization cellular localization organelle transport along microtubule transport establishment of vesicle localization intracellular transport establishment of localization vesicle transport along microtubule localization organelle localization establishment of localization in cell microtubule-based transport transport along microtubule cytoskeleton-dependent intracellular transport microtubule-based movement microtubule-based process import into cell endocytosis vesicle-mediated transport cell adhesion substrate adhesion-dependent cell spreading cell-substrate adhesion endoplasmic reticulum to Golgi vesicle-mediated transport Golgi vesicle transport cell migration cell motility defense response to bacterium biological process involved in interspecies interaction between organisms response to stimulus response to other organism defense response response to bacterium response to stress response to external stimulus response to external biotic stimulus response to biotic stimulus multicellular organismal process positive regulation of interleukin-8 production positive regulation of macromolecule biosynthetic process positive regulation of biosynthetic process cytokine production regulation of cytokine production regulation of multicellular organismal process regulation of biosynthetic process interleukin-8 production gene expression macromolecule biosynthetic process regulation of gene expression biosynthetic process positive regulation of gene expression positive regulation of multicellular organismal process regulation of macromolecule biosynthetic process positive regulation of cytokine production regulation of interleukin-8 production establishment of protein localization protein transport macromolecule localization intracellular protein localization intracellular protein transport establishment of melanosome localization cellular pigmentation pigment granule transport establishment of pigment granule localization pigmentation pigment granule localization melanosome transport melanosome localization membrane organization vesicle budding from membrane vesicle cargo loading vesicle organization COPII-coated vesicle cargo loading COPII-coated vesicle budding growth hormone secretion nitrogen compound transport secretion signaling regulation of hormone levels cell-cell signaling export from cell hormone secretion cell communication peptide transport peptide secretion secretion by cell peptide hormone secretion signal release hormone transport regulation of biological quality Golgi organization endomembrane system organization	cellular anatomical structure endomembrane system membrane-bounded organelle intracellular anatomical structure pigment granule intracellular vesicle intracellular membrane-bounded organelle intracellular organelle melanosome cytoplasmic vesicle organelle cytoplasm vesicle extracellular exosome cellular anatomical structure endomembrane system membrane-bounded organelle intracellular anatomical structure pigment granule intracellular vesicle intracellular membrane-bounded organelle intracellular organelle melanosome cytoplasmic vesicle organelle cytoplasm vesicle extracellular exosome extracellular vesicle extracellular organelle extracellular region extracellular space extracellular membrane-bounded organelle cytosol early endosome endosome Golgi apparatus Golgi membrane membrane bounding membrane of organelle organelle membrane transport vesicle transport vesicle membrane cytoplasmic vesicle membrane vesicle membrane endoplasmic reticulum
C, F	ADP-ribosylation factor 6	thioesterase binding protein binding 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 protein-macromolecule adaptor activity molecular adaptor activity signaling adaptor activity thioesterase binding protein binding 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 protein-macromolecule adaptor activity molecular adaptor activity signaling adaptor activity 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 G protein activity molecular function regulator activity	regulation of localization regulation of biological process regulation of protein localization biological regulation negative regulation of biological process localization negative regulation of protein localization to cell surface protein localization to cell surface macromolecule localization regulation of protein localization to cell surface intracellular protein localization negative regulation of protein localization cellular response to stimulus regulation of signaling regulation of localization regulation of biological process regulation of protein localization biological regulation negative regulation of biological process localization negative regulation of protein localization to cell surface protein localization to cell surface macromolecule localization regulation of protein localization to cell surface intracellular protein localization negative regulation of protein localization cellular response to stimulus regulation of signaling small GTPase-mediated signal transduction regulation of cellular process response to stimulus signaling regulation of small GTPase mediated signal transduction Rac protein signal transduction regulation of signal transduction intracellular signal transduction regulation of Rac protein signal transduction cell communication regulation of intracellular signal transduction regulation of response to stimulus intracellular signaling cassette regulation of cell communication cellular process signal transduction cell division positive regulation of protein localization to plasma membrane cellular localization positive regulation of biological process regulation of protein localization to membrane positive regulation of cellular process positive regulation of protein localization to cell periphery protein localization to cell periphery protein localization to plasma membrane positive regulation of protein localization to membrane regulation of protein localization to cell periphery localization within membrane protein localization to membrane regulation of cellular localization positive regulation of protein localization regulation of protein localization to plasma membrane establishment of cell polarity establishment of epithelial cell polarity establishment or maintenance of cell polarity regulation of neuron projection development multicellular organismal process regulation of cellular component organization regulation of developmental process cellular developmental process cell projection organization cell development neuron projection development cellular component organization neurogenesis multicellular organism development neuron differentiation dendrite development cell differentiation anatomical structure development negative regulation of cellular process cellular component organization or biogenesis negative regulation of cell projection organization system development developmental process plasma membrane bounded cell projection organization negative regulation of cellular component organization regulation of cell projection organization negative regulation of developmental process nervous system development negative regulation of neuron projection development negative regulation of dendrite development generation of neurons regulation of dendrite development neuron development regulation of plasma membrane bounded cell projection organization cellular response to endogenous stimulus cellular response to growth factor stimulus response to endogenous stimulus cellular response to nerve growth factor stimulus response to nerve growth factor response to growth factor protein localization to cleavage furrow protein localization to cell division site positive regulation of cellular component organization positive regulation of neuron projection development positive regulation of cell projection organization import into cell transport negative regulation of transport negative regulation of endocytosis vesicle-mediated transport regulation of endocytosis negative regulation of receptor-mediated endocytosis regulation of transport regulation of receptor-mediated endocytosis regulation of vesicle-mediated transport establishment of localization endocytosis receptor-mediated endocytosis regulation of dendritic spine development dendritic spine development organelle organization actin cytoskeleton organization cortical actin cytoskeleton organization cortical cytoskeleton organization actin filament-based process cytoskeleton organization positive regulation of locomotion regulation of cell motility regulation of keratinocyte migration positive regulation of cell migration positive regulation of epithelial cell migration tissue migration ameboidal-type cell migration positive regulation of cell motility regulation of cell migration cell migration regulation of multicellular organismal process epithelial cell migration cell motility regulation of epithelial cell migration locomotion epithelium migration regulation of locomotion positive regulation of keratinocyte migration keratinocyte migration cell adhesion cellular component disassembly regulation of focal adhesion disassembly focal adhesion disassembly cell junction disassembly cell-substrate junction disassembly positive regulation of cell-substrate junction organization cell junction organization positive regulation of focal adhesion disassembly cell-substrate junction organization regulation of cell-substrate junction organization hepaticobiliary system development gland development animal organ development liver development maintenance of synapse structure postsynapse organization cellular component maintenance maintenance of postsynaptic density structure cell junction maintenance maintenance of postsynaptic specialization structure postsynaptic density organization synapse organization postsynaptic specialization organization synaptic vesicle endocytosis synaptic vesicle cycle presynaptic endocytosis vesicle-mediated transport in synapse synaptic vesicle recycling establishment of localization in cell protein localization to endosome protein localization to organelle regulation of presynapse assembly cellular component biogenesis cellular component assembly regulation of presynapse organization cell junction assembly regulation of synapse structure or activity regulation of synapse assembly regulation of biological quality presynapse organization regulation of cellular component biogenesis regulation of cell junction assembly regulation of synapse organization synapse assembly presynapse assembly positive regulation of cell division cytoskeleton-dependent cytokinesis regulation of mitotic cytokinetic process positive regulation of mitotic cytokinesis mitotic cytokinetic process mitotic cytokinesis mitotic cell cycle regulation of cell division regulation of mitotic cytokinesis positive regulation of cytokinesis positive regulation of mitotic cytokinetic process positive regulation of cell cycle process cell cycle regulation of cell cycle cell cycle process regulation of cytokinesis regulation of cell cycle process cytokinesis regulation of cytokinetic process positive regulation of cell cycle mitotic cell cycle process cytokinetic process establishment of protein localization intracellular transport protein transport intracellular protein 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 secretion regulation of establishment of protein localization establishment of protein localization to extracellular region export from cell regulation of protein transport protein secretion positive regulation of protein secretion regulation of protein secretion regulation of secretion positive regulation of transport myeloid cell apoptotic process erythrocyte apoptotic process apoptotic process cell death programmed cell death ruffle organization plasma membrane bounded cell projection assembly ruffle assembly cell projection assembly hepatocyte apoptotic process epithelial cell apoptotic process positive regulation of organelle organization regulation of cytoskeleton organization regulation of actin filament-based process regulation of cellular component size regulation of protein-containing complex assembly positive regulation of protein-containing complex assembly positive regulation of protein polymerization protein-containing complex assembly regulation of actin filament polymerization protein polymerization actin polymerization or depolymerization regulation of actin filament organization actin filament polymerization protein-containing complex organization positive regulation of cellular component biogenesis positive regulation of cytoskeleton organization regulation of actin polymerization or depolymerization actin filament organization positive regulation of supramolecular fiber organization regulation of organelle organization regulation of protein polymerization regulation of actin filament length regulation of actin cytoskeleton organization regulation of supramolecular fiber organization supramolecular fiber organization positive regulation of actin filament polymerization regulation of anatomical structure size filopodium assembly regulation of cell projection assembly regulation of filopodium assembly regulation of plasma membrane bounded cell projection assembly endocytic recycling endosomal transport vesicle-mediated transport to the plasma membrane	cellular anatomical structure membrane extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle extracellular space vesicle extracellular membrane-bounded organelle intracellular anatomical structure cytoplasm cytosol cellular anatomical structure membrane extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle extracellular space vesicle extracellular membrane-bounded organelle intracellular anatomical structure cytoplasm cytosol intracellular vesicle intracellular membrane-bounded organelle intracellular organelle cytoplasmic vesicle endocytic vesicle synapse cell junction glutamatergic synapse Golgi apparatus endomembrane system ruffle cell projection cell leading edge plasma membrane bounded cell projection postsynapse midbody anchoring junction focal adhesion cell-substrate junction cell periphery cell cortex plasma membrane presynapse cell division site cleavage furrow plasma membrane region endosome membrane endosome recycling endosome cytoplasmic vesicle membrane bounding membrane of organelle recycling endosome membrane vesicle membrane organelle membrane early endosome early endosome membrane Flemming body filopodium membrane actin-based cell projection filopodium cell projection membrane
A, D	EspG protein	cysteine-type peptidase activity peptidase activity catalytic activity, acting on a protein cysteine-type endopeptidase activity hydrolase activity catalytic activity endopeptidase activity	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B, E	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
B, E	IPR005225	Small GTP-binding domain	Domain
B, E	IPR001806	Small GTPase	Family
B, E	IPR050227	Ras-related protein Rab	Family
B, E	IPR057289	Rab1/Ypt1	Family
C, F	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
C, F	IPR006689	Small GTPase superfamily, ARF/SAR type	Family
C, F	IPR041838	ADP-ribosylation factor 6	Family
C, F	IPR005225	Small GTP-binding domain	Domain
C, F	IPR024156	Small GTPase superfamily, ARF type	Family
A, D	IPR043098	Cysteine protease, VirA/EspG, N-terminal	Homologous Superfamily
A, D	IPR009669	Cysteine protease, VirA/EspG	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
B, E	Pharos: P62820	atrial fibrillation lung cancer myopathy pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia large cell medulloblastoma medulloblastoma osteosarcoma plasma cell myeloma lung adenocarcinoma metabolic syndrome X ovarian cancer Sjogren syndrome
C, F	Pharos: P62330	astrocytic tumor juvenile dermatomyositis osteosarcoma psoriasis esophageal adenocarcinoma malignant pancreatic neoplasm ovarian cancer glioblastoma myopathy pancreatic intraductal papillary-mucinous neoplasm

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.