5Z2M

Structure of Orp1L/Rab7 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

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
B [auth A]	d5z2ma_	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	G proteins	automated matches	Mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
C	d5z2mc_	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	G proteins	automated matches	Mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
A [auth B]	d5z2mb1	Alpha and beta proteins (a+b)	beta-hairpin-alpha-hairpin repeat	Ankyrin repeat	automated matches	automated matches	Mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
A [auth B]	d5z2mb2	Artifacts	Tags	Tags	Tags	N-terminal Tags	Mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
D	d5z2md1	Alpha and beta proteins (a+b)	beta-hairpin-alpha-hairpin repeat	Ankyrin repeat	automated matches	automated matches	Mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
D	d5z2md2	Artifacts	Tags	Tags	Tags	N-terminal Tags	Mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A [auth B]	SCOP2B Superfamily	Ankyrin repeat	8084066	3000154	SCOP2B (2022-06-29)
D	SCOP2 Family	Ankyrin repeat	8084065	4000366	SCOP2 (2022-06-29)
D	SCOP2 Superfamily	Ankyrin repeat	8084066	3000154	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 A]	Ras	e5z2mA1	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)
C	Ras	e5z2mC1	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)
A [auth B]	Ank_2	e5z2mB1	A: alpha superhelices	X: Repetitive alpha hairpins	H: Ankyrin repeat (From Topology)	T: Ankyrin repeat	F: Ank_2	ECOD (1.6)
D	Ank_2	e5z2mD1	A: alpha superhelices	X: Repetitive alpha hairpins	H: Ankyrin repeat (From Topology)	T: Ankyrin repeat	F: Ank_2	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B [auth A]	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
C	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
A [auth B]	1.25.40.20	Mainly Alpha	Alpha Horseshoe	Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat	Ankyrin repeat-containing domain	CATH (4.3.0)
D	1.25.40.20	Mainly Alpha	Alpha Horseshoe	Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat	Ankyrin repeat-containing domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B [auth A], C	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
A [auth B], D	PF12796	Ankyrin repeats (3 copies) (Ank_2)	Ankyrin repeats (3 copies)	-	Repeat

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B [auth A], C	Ras-related protein Rab-7a	small GTPase binding protein binding binding enzyme binding GTPase binding 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 small GTPase binding protein binding binding enzyme binding GTPase binding 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 ion binding organic cyclic compound binding purine nucleotide binding anion binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding GDP 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	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 protein localization establishment of protein localization nitrogen compound transport establishment of protein localization to plasma membrane endocytic recycling cellular macromolecule 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 cellular catabolic process catabolic process lipophagy macroautophagy cellular metabolic process 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 regulation of protein metabolic process positive regulation of biological process primary metabolic process regulation of macromolecule metabolic process protein catabolic process regulation of catabolic process positive regulation of protein catabolic process macromolecule catabolic process regulation of primary metabolic process positive regulation of catabolic process positive regulation of metabolic process positive regulation of macromolecule metabolic process protein metabolic process macromolecule metabolic process regulation of metabolic process regulation of protein catabolic process 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 process 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 cellular anatomical entity intracellular membrane-bounded organelle intracellular organelle organelle envelope mitochondrial envelope organelle cytoplasm organelle membrane cytosol membrane-bounded organelle mitochondrial membrane intracellular anatomical structure mitochondrion membrane cellular anatomical entity intracellular membrane-bounded organelle intracellular organelle organelle envelope mitochondrial envelope organelle 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 lamellar body secretory granule alveolar lamellar body protein-containing complex membrane protein complex retromer complex phagophore assembly site membrane phagophore assembly site lipid droplet intracellular non-membrane-bounded organelle non-membrane-bounded organelle
A [auth B], D	Oxysterol-binding protein-related protein 1	sterol binding binding organic cyclic compound binding alcohol binding steroid binding lipid binding cholesterol binding small molecule binding	localization transport macromolecule localization lipid localization lipid transport establishment of localization	intracellular anatomical structure cytoplasm cellular anatomical entity cytosol cell periphery plasma membrane membrane membrane-bounded organelle endosome intracellular vesicle intracellular membrane-bounded organelle endomembrane system intracellular organelle cytoplasmic vesicle intracellular anatomical structure cytoplasm cellular anatomical entity cytosol cell periphery plasma membrane membrane membrane-bounded organelle endosome intracellular vesicle intracellular membrane-bounded organelle endomembrane system intracellular organelle cytoplasmic vesicle organelle late endosome vesicle organelle membrane contact site perinuclear endoplasmic reticulum perinuclear region of cytoplasm endoplasmic reticulum

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B [auth A], C	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
B [auth A], C	IPR005225	Small GTP-binding domain	Domain
B [auth A], C	IPR001806	Small GTPase	Family
A [auth B], D	IPR002110	Ankyrin repeat	Repeat
A [auth B], D	IPR001849	Pleckstrin homology domain	Domain
A [auth B], D	IPR018494	Oxysterol-binding protein, conserved site	Conserved Site
A [auth B], D	IPR036770	Ankyrin repeat-containing domain superfamily	Homologous Superfamily
A [auth B], D	IPR037239	Oxysterol-binding protein superfamily	Homologous Superfamily
A [auth B], D	IPR000648	Oxysterol-binding protein	Family
A [auth B], D	IPR011993	PH-like domain superfamily	Homologous Superfamily

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.