5O74

Crystal structure of human Rab1b covalently bound to the GEF domain of DrrA/SidM from Legionella pneumophila in the presence of GDP

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	d5o74b_	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)
D	d5o74d_	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)
F	d5o74f_	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)
H	d5o74h_	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)
J	d5o74j_	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)
L	d5o74l_	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	8057458	3002022	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Ras-like P-loop GTPases	8057458	3002022	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Ras-like P-loop GTPases	8057458	3002022	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	Ras-like P-loop GTPases	8057458	3002022	SCOP2B (2022-06-29)
J	SCOP2B Superfamily	Ras-like P-loop GTPases	8057458	3002022	SCOP2B (2022-06-29)
L	SCOP2B Superfamily	Ras-like P-loop GTPases	8057458	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)
A	SidM_DrrA_GEF	e5o74A1	A: alpha arrays	X: SidM Rab1-activation domain (From Topology)	H: SidM Rab1-activation domain (From Topology)	T: SidM Rab1-activation domain	F: SidM_DrrA_GEF	ECOD (1.6)
C	SidM_DrrA_GEF	e5o74C1	A: alpha arrays	X: SidM Rab1-activation domain (From Topology)	H: SidM Rab1-activation domain (From Topology)	T: SidM Rab1-activation domain	F: SidM_DrrA_GEF	ECOD (1.6)
E	SidM_DrrA_GEF	e5o74E1	A: alpha arrays	X: SidM Rab1-activation domain (From Topology)	H: SidM Rab1-activation domain (From Topology)	T: SidM Rab1-activation domain	F: SidM_DrrA_GEF	ECOD (1.6)
G	SidM_DrrA_GEF	e5o74G1	A: alpha arrays	X: SidM Rab1-activation domain (From Topology)	H: SidM Rab1-activation domain (From Topology)	T: SidM Rab1-activation domain	F: SidM_DrrA_GEF	ECOD (1.6)
I	SidM_DrrA_GEF	e5o74I1	A: alpha arrays	X: SidM Rab1-activation domain (From Topology)	H: SidM Rab1-activation domain (From Topology)	T: SidM Rab1-activation domain	F: SidM_DrrA_GEF	ECOD (1.6)
K	SidM_DrrA_GEF	e5o74K1	A: alpha arrays	X: SidM Rab1-activation domain (From Topology)	H: SidM Rab1-activation domain (From Topology)	T: SidM Rab1-activation domain	F: SidM_DrrA_GEF	ECOD (1.6)
B	Ras	e5o74B1	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	e5o74D1	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)
F	Ras	e5o74F1	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)
H	Ras	e5o74H1	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)
J	Ras	e5o74J1	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)
L	Ras	e5o74L1	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)
A	1.20.1260.70	Mainly Alpha	Up-down Bundle	Ferritin		CATH (4.3.0)
C	1.20.1260.70	Mainly Alpha	Up-down Bundle	Ferritin		CATH (4.3.0)
E	1.20.1260.70	Mainly Alpha	Up-down Bundle	Ferritin		CATH (4.3.0)
G	1.20.1260.70	Mainly Alpha	Up-down Bundle	Ferritin		CATH (4.3.0)
I	1.20.1260.70	Mainly Alpha	Up-down Bundle	Ferritin		CATH (4.3.0)
K	1.20.1260.70	Mainly Alpha	Up-down Bundle	Ferritin		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)
D	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	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)
H	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
J	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
L	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, G, I A, C, E, G, I, K	PF20851	SidM, Rab1-activation domain (SidM_Rab1-act)	SidM, Rab1-activation domain	This domain is found in the type IV virulence effector SidM/DrrA from Legionella pneumophila. This protein has dual GEF and GDF activity specifically toward Rab1, a key regulator for endoplasmic reticulum (ER)-to-Golgi vesicle trafficking. SidM consi ...	This domain is found in the type IV virulence effector SidM/DrrA from Legionella pneumophila. This protein has dual GEF and GDF activity specifically toward Rab1, a key regulator for endoplasmic reticulum (ER)-to-Golgi vesicle trafficking. SidM consists of an N-terminal helical domain, a Rab1-activation domain (this entry), and a C- terminal phosphatidylinositol 4-phosphate-binding (P4M) domain (Pfam:PF14860). The Rab1-activation domain strongly interacts with Rab1 switch regions leading to substantial conformational changes on SidM binding. This domain is organized into two layers of helices [1,3].	Domain
B, D, F, H, J B, D, F, H, J, L	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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, C, E, G, I A, C, E, G, I, K	Multifunctional virulence effector protein DrrA	binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding small GTPase binding protein binding enzyme binding GTPase binding protein guanylyltransferase activity guanylyltransferase activity transferase activity nucleotidyltransferase activity catalytic activity transferase activity, transferring phosphorus-containing groups GTPase regulator activity enzyme regulator activity guanyl-nucleotide exchange factor activity nucleoside-triphosphatase regulator activity molecular function regulator activity phospholipid binding lipid binding phosphatidylinositol phosphate binding phosphatidylinositol-4-phosphate binding phosphatidylinositol binding adenylyltransferase activity AMPylase activity	regulation of molecular function regulation of catalytic activity regulation of hydrolase activity biological regulation regulation of GTPase activity protein nucleotidylation protein adenylylation macromolecule modification metabolic process primary metabolic process protein metabolic process macromolecule metabolic process protein modification process protein guanylylation	membrane cellular anatomical entity extracellular region host intracellular membrane-bounded organelle host cellular component host intracellular part host cell membrane host cell cytoplasmic vesicle membrane host cell cytoplasm part host intracellular organelle host cell cytoplasmic vesicle host cell cytoplasm host cell part host intracellular region
B, D, F, H, J B, D, F, H, J, L	Ras-related protein Rab-1B	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 binding guanyl nucleotide binding GTP binding nucleotide binding guanyl ribonucleotide 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 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	protein localization cellular localization establishment of protein localization nitrogen compound transport transport intracellular transport establishment of localization localization protein transport establishment of localization in cell cellular macromolecule localization macromolecule localization cellular process intracellular protein transport protein localization cellular localization establishment of protein localization nitrogen compound transport transport intracellular transport establishment of localization localization protein transport establishment of localization in cell cellular macromolecule localization macromolecule localization cellular process intracellular protein transport virion assembly viral process viral life cycle autophagosome assembly catabolic process organelle assembly vacuole organization macroautophagy cellular metabolic process autophagy autophagosome organization cellular component biogenesis cellular component organization cellular catabolic process organelle organization cellular component assembly metabolic process cellular component organization or biogenesis process utilizing autophagic mechanism regulation of biological 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 regulation of cellular component organization regulation of cellular process regulation of autophagosome assembly regulation of vacuole organization regulation of cellular component biogenesis regulation of organelle organization regulation of organelle assembly endoplasmic reticulum to Golgi vesicle-mediated transport Golgi vesicle transport vesicle-mediated transport Golgi organization endomembrane system organization	cellular anatomical entity endomembrane system membrane-bounded organelle intracellular organelle intracellular anatomical structure Golgi apparatus organelle cytoplasm intracellular membrane-bounded organelle Golgi membrane membrane bounding membrane of organelle organelle membrane endoplasmic reticulum-Golgi intermediate compartment membrane cellular anatomical entity endomembrane system membrane-bounded organelle intracellular organelle intracellular anatomical structure Golgi apparatus organelle cytoplasm intracellular membrane-bounded organelle Golgi membrane membrane bounding membrane of organelle organelle membrane endoplasmic reticulum-Golgi intermediate compartment membrane endoplasmic reticulum-Golgi intermediate compartment extracellular exosome extracellular vesicle extracellular organelle extracellular region extracellular space vesicle extracellular membrane-bounded organelle cytosol perinuclear region of cytoplasm phagophore assembly site membrane phagophore assembly site transport vesicle intracellular vesicle cytoplasmic vesicle organelle subcompartment endoplasmic reticulum subcompartment nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum endoplasmic reticulum membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, C, E, G, I A, C, E, G, I, K	IPR048718	SidM, Rab1-activation domain	Domain
A, C, E, G, I A, C, E, G, I, K	IPR038346	DrrA, PI4P binding domain superfamily	Homologous Superfamily
A, C, E, G, I A, C, E, G, I, K	IPR028057	DrrA phosphatidylinositol 4-phosphate binding domain	Domain
A, C, E, G, I A, C, E, G, I, K	IPR048717	SidM, N-terminal domain	Domain
A, C, E, G, I A, C, E, G, I, K	IPR033784	SidM, Rab1-activation domain, Legionella pneumophila	Domain
B, D, F, H, J B, D, F, H, J, L	IPR005225	Small GTP-binding domain	Domain
B, D, F, H, J B, D, F, H, J, L	IPR001806	Small GTPase	Family
B, D, F, H, J B, D, F, H, J, L	IPR050227	Ras-related protein Rab	Family
B, D, F, H, J B, D, F, H, J, L	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
B, D, F, H, J B, D, F, H, J, L	Pharos: Q9H0U4	astrocytic tumor coronary artery disease ovarian carcinoma bipolar disorder gout prostate carcinoma breast carcinoma myocardial ischemia

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 R01GM133198.