1VG9 | pdb_00001vg9

The crystal structures of the REP-1 protein in complex with C-terminally truncated Rab7 protein

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)
H	d1vg9h_	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	G proteins	Rab7	Norway rat (Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)
F	d1vg9f_	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	G proteins	Rab7	Norway rat (Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)
D	d1vg9d_	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	G proteins	Rab7	Norway rat (Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)
B	d1vg9b_	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	G proteins	Rab7	Norway rat (Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)
G	d1vg9g1	Alpha and beta proteins (a/b)	FAD/NAD(P)-binding domain	FAD/NAD(P)-binding domain	GDI-like N domain	Rab escort protein 1	Norway rat (Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)
G	d1vg9g2	Alpha and beta proteins (a+b)	FAD-linked reductases, C-terminal domain	FAD-linked reductases, C-terminal domain	GDI-like	Rab escort protein 1	Norway rat (Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)
E	d1vg9e1	Alpha and beta proteins (a/b)	FAD/NAD(P)-binding domain	FAD/NAD(P)-binding domain	GDI-like N domain	Rab escort protein 1	Norway rat (Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)
E	d1vg9e2	Alpha and beta proteins (a+b)	FAD-linked reductases, C-terminal domain	FAD-linked reductases, C-terminal domain	GDI-like	Rab escort protein 1	Norway rat (Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)
C	d1vg9c1	Alpha and beta proteins (a/b)	FAD/NAD(P)-binding domain	FAD/NAD(P)-binding domain	GDI-like N domain	Rab escort protein 1	Norway rat (Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)
C	d1vg9c2	Alpha and beta proteins (a+b)	FAD-linked reductases, C-terminal domain	FAD-linked reductases, C-terminal domain	GDI-like	Rab escort protein 1	Norway rat (Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)
A	d1vg9a1	Alpha and beta proteins (a/b)	FAD/NAD(P)-binding domain	FAD/NAD(P)-binding domain	GDI-like N domain	Rab escort protein 1	Norway rat (Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)
A	d1vg9a2	Alpha and beta proteins (a+b)	FAD-linked reductases, C-terminal domain	FAD-linked reductases, C-terminal domain	GDI-like	Rab escort protein 1	Norway rat (Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
H	SCOP2B Superfamily	Ras-like P-loop GTPases	8079222	3002022	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Ras-like P-loop GTPases	8079222	3002022	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Ras-like P-loop GTPases	8079222	3002022	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Ras-like P-loop GTPases	8079222	3002022	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	Flavoreductase-like	8044604	3000055	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	GDI isoprenoid-binding domain-like	8091669	3002533	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Flavoreductase-like	8044604	3000055	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	GDI isoprenoid-binding domain-like	8091669	3002533	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Flavoreductase-like	8044604	3000055	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	GDI isoprenoid-binding domain-like	8091669	3002533	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	GDI isoprenoid-binding domain-like	8091669	3002533	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Flavoreductase-like	8044604	3000055	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)
H	Ras	e1vg9H1	A: alpha bundles	X: HTH	H: HTH	T: winged helix domain	F: Ras	ECOD (develop294)
F	Ras	e1vg9F1	A: alpha bundles	X: HTH	H: HTH	T: winged helix domain	F: Ras	ECOD (develop294)
D	Ras	e1vg9D1	A: alpha bundles	X: HTH	H: HTH	T: winged helix domain	F: Ras	ECOD (develop294)
B	Ras	e1vg9B1	A: alpha bundles	X: HTH	H: HTH	T: winged helix domain	F: Ras	ECOD (develop294)
G	tRNA-synt_2d	e1vg9G2	A: alpha bundles	X: barrel domains in phase 1 flagellin	H: Class II aaRS and biotin synthetases	T: Class II aaRS and biotin synthetases	F: tRNA-synt_2d	ECOD (develop294)
G	SOS1_NGEF_PH	e1vg9G4	A: alpha bundles	X: POZ domain	H: Rossmann-related	T: S-adenosyl-L-methionine-dependent methyltransferases	F: SOS1_NGEF_PH	ECOD (develop294)
E	GIDA	e1vg9E3	A: alpha bundles	X: Fusion glycoprotein F2	H: MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase	T: MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase	F: GIDA	ECOD (develop294)
C	GDI	e1vg9C1	A: alpha bundles	X: Lipocalins/Streptavidin	H: Fibronectin type I module-like	T: Fibronectin type I module	F: GDI	ECOD (develop294)
A	S-AdoMet_synt_N	e1vg9A3	A: alpha bundles	X: Fusion glycoprotein F2	H: MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase	T: MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase	F: S-AdoMet_synt_N	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
H	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)
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)
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)
G	3.30.519.10	Alpha Beta	2-Layer Sandwich	Guanine Nucleotide Dissociation Inhibitor	domain 2	CATH (4.3.0)
G	1.10.405.10	Mainly Alpha	Orthogonal Bundle	Guanine Nucleotide Dissociation Inhibitor	domain 1	CATH (4.3.0)
E	3.50.50.60	Alpha Beta	3-Layer(bba) Sandwich	FAD/NAD(P)-binding domain	FAD/NAD(P)-binding domain	CATH (4.3.0)
E	3.30.519.10	Alpha Beta	2-Layer Sandwich	Guanine Nucleotide Dissociation Inhibitor	domain 2	CATH (4.3.0)
E	1.10.405.10	Mainly Alpha	Orthogonal Bundle	Guanine Nucleotide Dissociation Inhibitor	domain 1	CATH (4.3.0)
C	3.50.50.60	Alpha Beta	3-Layer(bba) Sandwich	FAD/NAD(P)-binding domain	FAD/NAD(P)-binding domain	CATH (4.3.0)
C	3.30.519.10	Alpha Beta	2-Layer Sandwich	Guanine Nucleotide Dissociation Inhibitor	domain 2	CATH (4.3.0)
C	1.10.405.10	Mainly Alpha	Orthogonal Bundle	Guanine Nucleotide Dissociation Inhibitor	domain 1	CATH (4.3.0)
A	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	3.30.519.10	Alpha Beta	2-Layer Sandwich	Guanine Nucleotide Dissociation Inhibitor	domain 2	CATH (4.3.0)
A	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, D, F, H	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
A, C, E, G	PF00996	GDP dissociation inhibitor (GDI)	GDP dissociation inhibitor	-	Family
A, C, E, G	PF22603	RAE1/2 domain I, C-terminal region (RAE1_2_domI_C)	RAE1/2 domain I, C-terminal region	This entry represents the C-terminal region of domain I from Rab escort proteins 1/2 (RAE1/2, also known as Rab proteins geranylgeranyltransferase component A 1/2) which are the substrate-binding subunit of the Rab geranylgeranyltransferase (GGTase) ...	This entry represents the C-terminal region of domain I from Rab escort proteins 1/2 (RAE1/2, also known as Rab proteins geranylgeranyltransferase component A 1/2) which are the substrate-binding subunit of the Rab geranylgeranyltransferase (GGTase) complex [1,2]. These proteins bind unprenylated Rab proteins and presents the substrate peptide to the catalytic component B and remains bound to it after the geranylgeranyl transfer reaction.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B, D, F, H	Ras-related protein Rab-7	small GTPase binding protein binding binding enzyme binding GTPase binding cation binding ion binding metal ion binding small molecule binding pyrophosphatase activity GTPase activity ribonucleoside triphosphate phosphatase activity hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides hydrolase activity small GTPase binding protein binding binding enzyme binding GTPase binding cation binding ion binding metal ion 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 protein-containing complex binding retromer complex binding guanyl nucleotide binding GTP binding nucleotide binding guanyl ribonucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding purine nucleotide binding anion binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding GDP binding G protein activity molecular function regulator activity	homeostatic process biological regulation phagosome maturation intracellular pH reduction regulation of intracellular pH cellular component organization phagosome acidification organelle organization cellular homeostasis chemical homeostasis intracellular monoatomic cation homeostasis regulation of pH monoatomic ion homeostasis intracellular chemical homeostasis homeostatic process biological regulation phagosome maturation intracellular pH reduction regulation of intracellular pH cellular component organization phagosome acidification organelle organization cellular homeostasis chemical homeostasis intracellular monoatomic cation homeostasis regulation of pH monoatomic ion homeostasis intracellular chemical homeostasis cellular process regulation of biological quality cellular component organization or biogenesis monoatomic cation homeostasis regulation of cellular pH intracellular monoatomic ion homeostasis localization transport establishment of localization vesicle-mediated transport vesicle-mediated transport in synapse cellular localization intracellular transport endosomal transport cytosolic transport retrograde transport, endosome to Golgi establishment of localization in cell vesicle localization establishment of organelle localization organelle localization establishment of vesicle localization establishment of protein localization establishment of protein localization to plasma membrane endocytic recycling intracellular protein localization protein localization to cell periphery establishment of protein localization to membrane protein localization to plasma membrane localization within membrane protein localization to membrane vesicle-mediated transport to the plasma membrane endosome to plasma membrane protein transport protein transport macromolecule localization intracellular protein transport multicellular organismal process multicellular organismal-level homeostasis tissue remodeling bone remodeling anatomical structure homeostasis tissue homeostasis bone resorption catabolic process lipophagy macroautophagy autophagy metabolic process process utilizing autophagic mechanism membrane docking protein to membrane docking import into cell membrane fusion organelle membrane fusion vesicle organization cellular component biogenesis lysosome organization cellular component assembly phagolysosome assembly phagocytosis membrane organization vacuole organization organelle assembly lytic vacuole organization phagosome-lysosome fusion organelle fusion endocytosis vesicle fusion endosome to lysosome transport lysosomal transport vacuolar transport autophagosome assembly autophagosome organization exosomal secretion regulation of localization regulation of cellular process negative regulation of biological process negative regulation of transport secretion by cell regulation of secretion by cell negative regulation of secretion negative regulation of exocytosis negative regulation of exosomal secretion negative regulation of cellular process negative regulation of secretion by cell regulation of biological process secretion regulation of transport regulation of exosomal secretion export from cell regulation of vesicle-mediated transport extracellular exosome biogenesis regulation of secretion exocytosis extracellular vesicle biogenesis regulation of exocytosis positive regulation of protein metabolic process positive regulation of biological process macromolecule catabolic process regulation of primary metabolic process positive regulation of metabolic process positive regulation of macromolecule metabolic process protein metabolic process positive regulation of cellular process regulation of protein metabolic process primary metabolic process regulation of macromolecule metabolic process protein catabolic process regulation of catabolic process positive regulation of protein catabolic process positive regulation of catabolic process macromolecule metabolic process regulation of metabolic process regulation of protein catabolic process synaptic vesicle cycle synaptic vesicle endosomal processing synaptic vesicle recycling via endosome synaptic vesicle recycling lipid catabolic process lipid metabolic process biological process involved in interspecies interaction between organisms response to stimulus response to other organism response to bacterium response to external stimulus response to external biotic stimulus response to biotic stimulus exit from host cell viral process viral release from host cell viral life cycle biological process involved in interaction with host biological process involved in symbiotic interaction establishment of protein localization to vacuole neurotransmitter receptor transport, postsynaptic endosome to lysosome neurotransmitter receptor transport protein localization to vacuole protein-containing complex localization protein localization to lysosome establishment of protein localization to organelle protein localization to organelle positive regulation of secretion by cell positive regulation of exosomal secretion positive regulation of exocytosis positive regulation of secretion positive regulation of cellular component biogenesis regulation of cellular component biogenesis positive regulation of transport cellular response to stimulus signaling negative regulation of signaling negative regulation of ERBB signaling pathway regulation of signal transduction cell surface receptor protein tyrosine kinase signaling pathway negative regulation of cell communication cell communication regulation of epidermal growth factor receptor signaling pathway epidermal growth factor receptor signaling pathway epidermal growth factor catabolic process signal transduction enzyme-linked receptor protein signaling pathway regulation of signaling regulation of ERBB signaling pathway cell surface receptor signaling pathway negative regulation of response to stimulus negative regulation of signal transduction regulation of response to stimulus negative regulation of epidermal growth factor receptor signaling pathway ERBB signaling pathway regulation of cell communication protein targeting protein targeting to lysosome protein targeting to vacuole vesicle-mediated transport between endosomal compartments early endosome to late endosome transport regulation of viral process positive regulation of viral process	membrane-bounded organelle mitochondrial membrane intracellular anatomical structure mitochondrion membrane intracellular membrane-bounded organelle intracellular organelle organelle envelope cellular anatomical structure organelle mitochondrial envelope cytoplasm organelle membrane cytosol membrane-bounded organelle mitochondrial membrane intracellular anatomical structure mitochondrion membrane intracellular membrane-bounded organelle intracellular organelle organelle envelope cellular anatomical structure organelle mitochondrial envelope cytoplasm organelle membrane cytosol endosome membrane endosome intracellular vesicle late endosome membrane endomembrane system cytoplasmic vesicle membrane bounding membrane of organelle cytoplasmic vesicle vesicle membrane late endosome vesicle synapse cell junction glutamatergic synapse vacuolar membrane autophagosome membrane vacuole autophagosome phagocytic vesicle phagocytic vesicle membrane endocytic vesicle membrane endocytic vesicle lytic vacuole lytic vacuole membrane lysosomal membrane lysosome Golgi apparatus transport vesicle membrane presynapse synaptic vesicle synaptic vesicle membrane transport vesicle exocytic vesicle membrane secretory vesicle exocytic vesicle pigment granule chitosome melanosome melanosome membrane pigment granule membrane presynaptic endosome lamellar body secretory granule alveolar lamellar body protein-containing complex membrane protein complex retromer complex axon neuron projection axon terminus plasma membrane bounded cell projection cell projection distal axon terminal bouton neuron projection terminus phagophore assembly site membrane phagophore assembly site lipid droplet membraneless organelle intracellular membraneless organelle
A, C, E, G	Rab proteins geranylgeranyltransferase component A 1	small GTPase binding protein binding binding enzyme binding GTPase binding protein-containing complex binding GTPase regulator activity enzyme regulator activity GDP-dissociation inhibitor activity nucleoside-triphosphatase regulator activity molecular function regulator activity enzyme activator activity GTPase activator activity molecular function activator activity	cellular localization establishment of protein localization transport intracellular transport establishment of localization localization protein transport establishment of localization in cell macromolecule localization cellular process intracellular protein localization intracellular protein transport vesicle-mediated transport developmental process cellular localization establishment of protein localization transport intracellular transport establishment of localization localization protein transport establishment of localization in cell macromolecule localization cellular process intracellular protein localization intracellular protein transport vesicle-mediated transport developmental process multicellular organism development multicellular organismal process anatomical structure development vasculature development blood vessel development system development circulatory system development establishment of protein localization to membrane protein targeting localization within membrane protein targeting to membrane macromolecule modification protein prenylation protein geranylgeranylation metabolic process primary metabolic process protein metabolic process macromolecule metabolic process prenylation protein modification process 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	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol protein-containing complex catalytic complex Rab-protein geranylgeranyltransferase complex transferase complex membrane-bounded organelle intracellular organelle organelle nucleus intracellular membrane-bounded organelle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B, D, F, H	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
B, D, F, H	IPR005225	Small GTP-binding domain	Domain
B, D, F, H	IPR001806	Small GTPase	Family
A, C, E, G	IPR054420	RAE1/2 domain I, C-terminal region	Domain
A, C, E, G	IPR036188	FAD/NAD(P)-binding domain superfamily	Homologous Superfamily
A, C, E, G	IPR001738	Rab protein geranylgeranyltransferase component A	Family
A, C, E, G	IPR018203	GDP dissociation inhibitor	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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.