4FMB | pdb_00004fmb

VirA-Rab1 complex structure

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

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
F	SCOP2B Superfamily	Ras-like P-loop GTPases	8057282	3002022	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Ras-like P-loop GTPases	8057282	3002022	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Ras-like P-loop GTPases	8057282	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)
E	EspG_1st	e4fmbE1	A: a+b two layers	X: LEE-encoded effector EspG N-terminal domain-related (From Topology)	H: LEE-encoded effector EspG N-terminal domain-related (From Topology)	T: LEE-encoded effector EspG N-terminal domain-related	F: EspG_1st	ECOD (1.6)
E	EspG_2nd	e4fmbE2	A: a+b two layers	X: LEE-encoded effector EspG C-terminal domain-related (From Topology)	H: LEE-encoded effector EspG C-terminal domain-related (From Topology)	T: LEE-encoded effector EspG C-terminal domain-related	F: EspG_2nd	ECOD (1.6)
C	EspG_1st	e4fmbC1	A: a+b two layers	X: LEE-encoded effector EspG N-terminal domain-related (From Topology)	H: LEE-encoded effector EspG N-terminal domain-related (From Topology)	T: LEE-encoded effector EspG N-terminal domain-related	F: EspG_1st	ECOD (1.6)
C	EspG_2nd	e4fmbC2	A: a+b two layers	X: LEE-encoded effector EspG C-terminal domain-related (From Topology)	H: LEE-encoded effector EspG C-terminal domain-related (From Topology)	T: LEE-encoded effector EspG C-terminal domain-related	F: EspG_2nd	ECOD (1.6)
A	EspG_1st	e4fmbA1	A: a+b two layers	X: LEE-encoded effector EspG N-terminal domain-related (From Topology)	H: LEE-encoded effector EspG N-terminal domain-related (From Topology)	T: LEE-encoded effector EspG N-terminal domain-related	F: EspG_1st	ECOD (1.6)
A	EspG_2nd	e4fmbA2	A: a+b two layers	X: LEE-encoded effector EspG C-terminal domain-related (From Topology)	H: LEE-encoded effector EspG C-terminal domain-related (From Topology)	T: LEE-encoded effector EspG C-terminal domain-related	F: EspG_2nd	ECOD (1.6)
F	Ras	e4fmbF1	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)
D	Ras	e4fmbD1	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	Ras	e4fmbB1	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)
E	3.10.450.460	Alpha Beta	Roll	Nuclear Transport Factor 2	Chain: A,	CATH (4.3.0)
C	3.10.450.460	Alpha Beta	Roll	Nuclear Transport Factor 2	Chain: A,	CATH (4.3.0)
A	3.10.450.460	Alpha Beta	Roll	Nuclear Transport Factor 2	Chain: A,	CATH (4.3.0)
F	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
D	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
B	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, C, E	PF06872	EspG protein (EspG)	EspG protein	-	Family
B, D, F	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
A, C, E	Cysteine protease-like virA	cysteine-type peptidase activity peptidase activity catalytic activity, acting on a protein cysteine-type endopeptidase activity hydrolase activity catalytic activity endopeptidase activity	proteolysis metabolic process cellular process primary metabolic process protein metabolic process macromolecule metabolic process	cellular anatomical structure extracellular region
B, D, F	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	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 nitrogen compound transport 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 signaling hormone secretion cell communication peptide secretion secretion by cell amide transport signal release regulation of biological quality growth hormone secretion secretion regulation of hormone levels cell-cell signaling export from cell peptide transport peptide hormone secretion hormone transport 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

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, C, E	IPR043098	Cysteine protease, VirA/EspG, N-terminal	Homologous Superfamily
A, C, E	IPR009669	Cysteine protease, VirA/EspG	Family
B, D, F	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
B, D, F	IPR005225	Small GTP-binding domain	Domain
B, D, F	IPR001806	Small GTPase	Family
B, D, F	IPR050227	Ras-related protein Rab	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
B, D, F	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

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.