2BCG | pdb_00002bcg

Structure of doubly prenylated Ypt1:GDI complex

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
Membrane Protein Annotation: OPM

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
B [auth Y]	d2bcgy_	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	G proteins	GTPase Ytp1	baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
A [auth G]	d2bcgg1	Alpha and beta proteins (a/b)	FAD/NAD(P)-binding domain	FAD/NAD(P)-binding domain	GDI-like N domain	Guanine nucleotide dissociation inhibitor, GDI	baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
A [auth G]	d2bcgg3	Alpha and beta proteins (a+b)	FAD-linked reductases, C-terminal domain	FAD-linked reductases, C-terminal domain	GDI-like	Guanine nucleotide dissociation inhibitor, GDI	baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B [auth Y]	SCOP2 Family	Ras-like monodomain GTPases	8057263	4004043	SCOP2 (2022-06-29)
B [auth Y]	SCOP2 Superfamily	Ras-like P-loop GTPases	8057264	3002022	SCOP2 (2022-06-29)
A [auth G]	SCOP2 Family	GDI-like	8001399	4000126	SCOP2 (2022-06-29)
A [auth G]	SCOP2 Family	GDI isoprenoid-binding domain-like	8091666	4007752	SCOP2 (2022-06-29)
A [auth G]	SCOP2 Superfamily	Flavoreductase-like	8001400	3000055	SCOP2 (2022-06-29)
A [auth G]	SCOP2 Superfamily	GDI isoprenoid-binding domain-like	8091667	3002533	SCOP2 (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 [auth Y]	GBP	e2bcgY1	A: a/b three-layered sandwiches	X: HTH	H: HTH	T: winged helix domain	F: GBP	ECOD (v294.1)
A [auth G]	Methyltr_RsmB-F	e2bcgG1	A: a/b three-layered sandwiches	X: amino-terminal domain of OmpATb	H: amino-terminal domain of OmpATb	T: amino-terminal domain of OmpATb	F: Methyltr_RsmB-F	ECOD (v294.1)
A [auth G]	GDI	e2bcgG2	A: a/b three-layered sandwiches	X: Alkaline phosphatase-like	H: Rossmann-related	T: FAD/NAD(P)-binding domain	F: GDI	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B [auth Y]	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
A [auth G]	3.50.50.60	Alpha Beta	3-Layer(bba) Sandwich	FAD/NAD(P)-binding domain	FAD/NAD(P)-binding domain	CATH (4.3.0)
A [auth G]	3.30.519.10	Alpha Beta	2-Layer Sandwich	Guanine Nucleotide Dissociation Inhibitor	domain 2	CATH (4.3.0)
A [auth G]	1.10.405.10	Mainly Alpha	Orthogonal Bundle	Guanine Nucleotide Dissociation Inhibitor	domain 1	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B [auth Y]	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
B [auth Y]	GTP-binding protein YPT1	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 protein binding SNARE 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	catabolic process RNA metabolic process primary metabolic process nucleic acid metabolic process macromolecule catabolic process nucleobase-containing compound catabolic process nucleobase-containing compound metabolic process pre-mRNA catabolic process nucleic acid catabolic process metabolic process cellular process macromolecule metabolic process RNA catabolic process membrane organization catabolic process RNA metabolic process primary metabolic process nucleic acid metabolic process macromolecule catabolic process nucleobase-containing compound catabolic process nucleobase-containing compound metabolic process pre-mRNA catabolic process nucleic acid catabolic process metabolic process cellular process macromolecule metabolic process RNA catabolic process membrane organization vesicle budding from membrane cellular localization transport intracellular transport endoplasmic reticulum to Golgi vesicle-mediated transport establishment of localization vesicle-mediated transport cellular component organization vesicle organization localization intercellular transport organelle organization establishment of localization in cell cellular component organization or biogenesis COPII-coated vesicle budding Golgi vesicle transport early endosome to Golgi transport endosomal transport cytosolic transport retrograde transport, endosome to Golgi cellular response to stimulus regulation of cellular process response to stimulus signaling regulation of cellular response to stress regulation of response to endoplasmic reticulum stress endoplasmic reticulum unfolded protein response regulation of signal transduction intracellular signal transduction cell communication regulation of endoplasmic reticulum unfolded protein response cellular response to stress regulation of intracellular signal transduction regulation of response to stress response to stress signal transduction response to endoplasmic reticulum stress regulation of biological process regulation of signaling cellular response to topologically incorrect protein biological regulation cellular response to unfolded protein response to unfolded protein regulation of response to stimulus response to topologically incorrect protein regulation of cell communication Golgi vesicle budding protein-containing complex organization membrane fusion organelle membrane fusion cellular component biogenesis organelle fusion cellular component assembly protein-containing complex assembly SNARE complex assembly vesicle fusion autophagosome assembly organelle assembly vacuole organization macroautophagy autophagy autophagosome organization process utilizing autophagic mechanism membrane docking organelle localization by membrane tethering Golgi vesicle docking organelle localization vesicle docking establishment of protein localization protein transport macromolecule localization intracellular protein localization intracellular protein transport retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum protein targeting establishment of protein localization to vacuole protein localization to vacuole cytoplasm to vacuole targeting by the Cvt pathway establishment of protein localization to organelle protein localization to organelle vacuolar transport protein targeting to vacuole cellular component disassembly SNARE complex disassembly protein-containing complex disassembly localization within membrane endocytic recycling vesicle-mediated transport to the plasma membrane protein localization to phagophore assembly site reticulophagy	cellular anatomical structure endomembrane system membrane-bounded organelle intracellular organelle intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle Golgi apparatus cis-Golgi network Golgi apparatus subcompartment organelle subcompartment Golgi stack cellular anatomical structure endomembrane system membrane-bounded organelle intracellular organelle intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle Golgi apparatus cis-Golgi network Golgi apparatus subcompartment organelle subcompartment Golgi stack cytosol phagophore assembly site membrane membrane phagophore assembly site endoplasmic reticulum subcompartment nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum organelle membrane endoplasmic reticulum membrane cytoplasmic vesicle intracellular vesicle vesicle Golgi membrane bounding membrane of organelle
A [auth G]	Secretory pathway GDP dissociation inhibitor	GTPase regulator activity enzyme regulator activity GDP-dissociation inhibitor activity nucleoside-triphosphatase regulator activity Rab GDP-dissociation inhibitor activity molecular function regulator activity enzyme activator activity GTPase activator activity molecular function activator activity	localization transport cellular process establishment of localization vesicle-mediated transport cellular response to stimulus regulation of biological process small GTPase-mediated signal transduction regulation of cellular process response to stimulus signaling biological regulation intracellular signal transduction cell communication localization transport cellular process establishment of localization vesicle-mediated transport cellular response to stimulus regulation of biological process small GTPase-mediated signal transduction regulation of cellular process response to stimulus signaling biological regulation intracellular signal transduction cell communication intracellular signaling cassette signal transduction establishment of protein localization protein transport macromolecule localization intracellular protein localization	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B [auth Y]	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
B [auth Y]	IPR005225	Small GTP-binding domain	Domain
B [auth Y]	IPR001806	Small GTPase	Family
B [auth Y]	IPR050227	Ras-related protein Rab	Family
B [auth Y]	IPR057289	Rab1/Ypt1	Family
A [auth G]	IPR000806	Rab GDI protein	Family
A [auth G]	IPR018203	GDP dissociation inhibitor	Family
A [auth G]	IPR036188	FAD/NAD(P)-binding domain superfamily	Homologous Superfamily

Membrane Protein Annotation: OPM OPM Database Homepage

Chains	External Link	Type	Class	Superfamily	Family
B [auth Y]	OPM	Monotopic/peripheral	Alpha/Beta monotopic/peripheral	FAD/NAD(P)-binding domain	GDP dissociation inhibitor

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.