4ZDW

Crystal structure of the Rab GTPase Sec4p mutant - S29V in complex with Sec2p and 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

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d4zdwa_	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	G proteins	automated matches	Baker's yeast (Saccharomyces cerevisiae S288C ) [TaxId: 559292 ],	SCOPe (2.08)
C	d4zdwc1	Coiled coil proteins	Parallel coiled-coil	Sec2 N-terminal region	Sec2 N-terminal region	Rab guanine nucleotide exchange factor Sec2	Baker's yeast (Saccharomyces cerevisiae S288C ) [TaxId: 559292 ],	SCOPe (2.08)
C	d4zdwc2	Artifacts	Tags	Tags	Tags	N-terminal Tags	Baker's yeast (Saccharomyces cerevisiae S288C ) [TaxId: 559292 ],	SCOPe (2.08)
B	d4zdwb1	Coiled coil proteins	Parallel coiled-coil	Sec2 N-terminal region	Sec2 N-terminal region	Rab guanine nucleotide exchange factor Sec2	Baker's yeast (Saccharomyces cerevisiae S288C ) [TaxId: 559292 ],	SCOPe (2.08)
B	d4zdwb2	Artifacts	Tags	Tags	Tags	N-terminal Tags	Baker's yeast (Saccharomyces cerevisiae S288C ) [TaxId: 559292 ],	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	8057408	3002022	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Sec2 N-terminal region	8040018	3000591	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Sec2 N-terminal region	8040018	3000591	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	e4zdwA1	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	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
C	1.20.5.4880	Mainly Alpha	Up-down Bundle	Single alpha-helices involved in coiled-coils or other helix-helix interfaces		CATH (4.3.0)
B	1.20.5.4880	Mainly Alpha	Up-down Bundle	Single alpha-helices involved in coiled-coils or other helix-helix interfaces		CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	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, C	PF06428	GDP/GTP exchange factor Sec2p (Sec2p)	GDP/GTP exchange factor Sec2p	-	Coiled-coil

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Ras-related protein SEC4	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 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 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	membrane organization cellular component organization cytokinetic process cellular process cell cycle cytokinesis cell division cellular component organization or biogenesis membrane addition at site of cytokinesis cell cycle process Golgi to plasma membrane transport cellular localization post-Golgi vesicle-mediated transport transport membrane organization cellular component organization cytokinetic process cellular process cell cycle cytokinesis cell division cellular component organization or biogenesis membrane addition at site of cytokinesis cell cycle process Golgi to plasma membrane transport cellular localization post-Golgi vesicle-mediated transport transport localization within membrane establishment of localization vesicle-mediated transport vesicle-mediated transport to the plasma membrane localization Golgi vesicle transport protein localization establishment of protein localization nitrogen compound transport secretion establishment of protein localization to extracellular region export from cell protein secretion protein localization to extracellular region secretion by cell protein transport cellular macromolecule localization macromolecule localization cellular catabolic process catabolic process cellular metabolic process autophagy metabolic process process utilizing autophagic mechanism membrane fusion organelle membrane fusion vesicle organization organelle fusion organelle organization vesicle fusion sexual reproduction cellular developmental process cellular component assembly involved in morphogenesis reproductive process cell development developmental process involved in reproduction meiotic cell cycle process cellular component biogenesis cellular anatomical entity morphogenesis cellular component assembly sexual sporulation cell differentiation anatomical structure development developmental process sexual sporulation resulting in formation of a cellular spore reproductive process in single-celled organism meiotic cell cycle sporulation resulting in formation of a cellular spore anatomical structure morphogenesis ascospore formation ascospore-type prospore assembly anatomical structure formation involved in morphogenesis sporulation exocytosis	membrane-bounded organelle intracellular organelle intracellular anatomical structure mitochondrion organelle cytoplasm cellular anatomical entity intracellular membrane-bounded organelle incipient cellular bud site site of polarized growth vesicle endosome intracellular vesicle endomembrane system membrane-bounded organelle intracellular organelle intracellular anatomical structure mitochondrion organelle cytoplasm cellular anatomical entity intracellular membrane-bounded organelle incipient cellular bud site site of polarized growth vesicle endosome intracellular vesicle endomembrane system cytoplasmic vesicle cell projection mating projection cell tip mating projection tip cell pole plasma membrane bounded cell projection mitochondrial membrane membrane organelle outer membrane organelle envelope bounding membrane of organelle mitochondrial envelope mitochondrial outer membrane outer membrane organelle membrane cell periphery plasma membrane transport vesicle cellular bud neck cellular bud transport vesicle membrane cytoplasmic vesicle membrane vesicle membrane endoplasmic reticulum
B, C	Rab guanine nucleotide exchange factor SEC2	GTPase regulator activity enzyme regulator activity guanyl-nucleotide exchange factor activity nucleoside-triphosphatase regulator activity molecular function regulator activity binding phospholipid binding lipid binding phosphatidylinositol phosphate binding phosphatidylinositol-4-phosphate binding phosphatidylinositol binding identical protein binding protein binding	sporulation resulting in formation of a cellular spore developmental process anatomical structure morphogenesis anatomical structure formation involved in morphogenesis anatomical structure development sporulation cellular catabolic process catabolic process cellular metabolic process autophagy cellular process metabolic process process utilizing autophagic mechanism protein localization sporulation resulting in formation of a cellular spore developmental process anatomical structure morphogenesis anatomical structure formation involved in morphogenesis anatomical structure development sporulation cellular catabolic process catabolic process cellular metabolic process autophagy cellular process metabolic process process utilizing autophagic mechanism protein localization establishment of protein localization cellular localization nitrogen compound transport transport establishment of localization localization protein transport cellular macromolecule localization macromolecule localization sexual reproduction cellular developmental process cellular component assembly involved in morphogenesis reproductive process cell development ascospore-type prospore membrane formation developmental process involved in reproduction membrane biogenesis meiotic cell cycle process cellular component organization cellular component biogenesis cellular anatomical entity morphogenesis cellular component assembly sexual sporulation cell differentiation cellular component organization or biogenesis cell cycle cell cycle process membrane organization sexual sporulation resulting in formation of a cellular spore reproductive process in single-celled organism meiotic cell cycle membrane assembly ascospore formation ascospore-type prospore assembly secretion by cell exocytosis secretion export from cell vesicle-mediated transport	membrane-bounded organelle intracellular anatomical structure transport vesicle intracellular vesicle cellular anatomical entity intracellular membrane-bounded organelle endomembrane system intracellular organelle cytoplasmic vesicle Golgi to plasma membrane transport vesicle organelle secretory vesicle cytoplasm vesicle membrane-bounded organelle intracellular anatomical structure transport vesicle intracellular vesicle cellular anatomical entity intracellular membrane-bounded organelle endomembrane system intracellular organelle cytoplasmic vesicle Golgi to plasma membrane transport vesicle organelle secretory vesicle cytoplasm vesicle exocytic vesicle cell tip cell pole cellular bud cellular bud tip site of polarized growth cell projection mating projection mating projection tip plasma membrane bounded cell projection cytosol cellular bud neck

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR005225	Small GTP-binding domain	Domain
A	IPR001806	Small GTPase	Family
A	IPR050305	Small GTPase superfamily, Rab	Family
A	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
B, C	IPR009449	GDP/GTP exchange factor Sec2, N-terminal	Domain
B, C	IPR040351	Guanine nucleotide exchange factor RAB3IL/RAB3IP/Sec2	Family

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.