Annotations: 4Q9U

Crystal structure of the Rab5, Rabex-5delta and Rabaptin-5C21 complex

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

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	8054292	3002022	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	VPS9 domain	8043652	3001620	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	VPS9 domain	8043652	3001620	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)
F	RNase_T	e4q9uF1	A: beta barrels	X: alpha/beta-Hydrolases	H: alpha/beta-Hydrolases	T: alpha/beta-Hydrolases	F: RNase_T	ECOD (v294.2)
B	Ribosomal_S8e	e4q9uB1	A: beta barrels	X: Immunoglobulin-like beta-sandwich	H: Ribosomal protein L14-related	T: Ribosomal protein L14-related	F: Ribosomal_S8e	ECOD (v294.2)
E	MIF4G	e4q9uE1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: MIF4G	ECOD (v294.2)
A	DUF5601	e4q9uA1	A: beta barrels	X: OB-fold	H: Phage tail fiber protein trimerization domain	T: Phage tail fiber protein trimerization domain	F: DUF5601	ECOD (v294.2)
A	RPE65	e4q9uA2	A: beta barrels	X: OB-fold	H: Phage tail fiber protein trimerization domain	T: Phage tail fiber protein trimerization domain	F: RPE65	ECOD (v294.2)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B, F	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, E	PF18151	Domain of unknown function (DUF5601) (DUF5601)	Domain of unknown function (DUF5601)	This domain is found in the catalytic core RABEX-5 present in Homo sapiens. RABEX, also known as Rab GTPase exchange factors, regulate endocytic trafficking through activation of the Rab families RAB5, RAB21 and RAB22. The domain is helical in nature ...	This domain is found in the catalytic core RABEX-5 present in Homo sapiens. RABEX, also known as Rab GTPase exchange factors, regulate endocytic trafficking through activation of the Rab families RAB5, RAB21 and RAB22. The domain is helical in nature [1].	Domain
A, E	PF02204	Vacuolar sorting protein 9 (VPS9) domain (VPS9)	Vacuolar sorting protein 9 (VPS9) domain	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C, D, G, H	Rab GTPase-binding effector protein 1	protein binding binding protein domain specific binding identical protein binding protein homodimerization activity protein dimerization activity molecular function activator activity molecular function regulator activity signaling receptor regulator activity growth factor activity receptor ligand activity signaling receptor activator activity GTPase regulator activity enzyme regulator activity protein binding binding protein domain specific binding identical protein binding protein homodimerization activity protein dimerization activity molecular function activator activity molecular function regulator activity signaling receptor regulator activity growth factor activity receptor ligand activity signaling receptor activator activity GTPase regulator activity enzyme regulator activity enzyme activator activity GTPase activator activity nucleoside-triphosphatase regulator activity	membrane organization cellular component organization membrane fusion cellular process cellular component organization or biogenesis 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 membrane organization cellular component organization membrane fusion cellular process cellular component organization or biogenesis 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 import into cell endocytosis establishment of protein localization protein transport macromolecule localization intracellular protein localization apoptotic process cell death programmed cell death protein localization to cell periphery protein localization to cilium protein localization to membrane protein localization to ciliary membrane protein localization to organelle regulation of localization regulation of cellular process regulation of cellular component organization receptor internalization postsynaptic neurotransmitter receptor internalization regulation of receptor internalization vesicle-mediated transport in synapse establishment of localization in cell regulation of postsynaptic neurotransmitter receptor internalization regulation of biological quality regulation of endocytosis regulation of biological process regulation of transport biological regulation regulation of receptor-mediated endocytosis regulation of vesicle-mediated transport neurotransmitter receptor internalization regulation of postsynaptic membrane neurotransmitter receptor levels postsynaptic endocytosis receptor-mediated endocytosis	membrane-bounded organelle intracellular anatomical structure early endosome endosome intracellular vesicle intracellular membrane-bounded organelle endomembrane system intracellular organelle cellular anatomical structure cytoplasmic vesicle organelle cytoplasm vesicle endosome membrane membrane-bounded organelle intracellular anatomical structure early endosome endosome intracellular vesicle intracellular membrane-bounded organelle endomembrane system intracellular organelle cellular anatomical structure cytoplasmic vesicle organelle cytoplasm vesicle endosome membrane membrane early endosome membrane cytoplasmic vesicle membrane bounding membrane of organelle vesicle membrane organelle membrane recycling endosome cytosol endocytic vesicle protein-containing complex synapse cell junction glutamatergic synapse
B, F	Ras-related protein Rab-5A	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 binding guanyl nucleotide binding GTP binding nucleotide binding guanyl ribonucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate 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 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 GDP binding G protein activity molecular function regulator activity	cellular component organization regulation of cellular component size regulation of vesicle size biological regulation cellular process cellular component organization or biogenesis regulation of biological quality regulation of endosome size regulation of anatomical structure size localization transport plasma membrane to endosome transport establishment of localization vesicle-mediated transport cellular component organization regulation of cellular component size regulation of vesicle size biological regulation cellular process cellular component organization or biogenesis regulation of biological quality regulation of endosome size regulation of anatomical structure size localization transport plasma membrane to endosome transport establishment of localization vesicle-mediated transport import into cell receptor internalization receptor-mediated endocytosis endocytosis cellular response to stimulus regulation of biological process regulation of cellular process cell surface receptor signaling pathway response to stimulus signaling canonical Wnt signaling pathway cell communication signal transduction Wnt signaling pathway phagocytosis catabolic process regulation of cellular component organization macroautophagy autophagy autophagosome organization cellular component biogenesis cellular component assembly process utilizing autophagic mechanism autophagosome assembly organelle assembly vacuole organization regulation of autophagosome assembly regulation of vacuole organization regulation of cellular component biogenesis regulation of organelle organization organelle organization regulation of organelle assembly metabolic process protein localization to endosome protein localization to organelle macromolecule localization protein localization to early endosome intracellular protein localization regulation of neuronal synaptic plasticity regulation of synaptic plasticity trans-synaptic signaling regulation of signaling regulation of long-term neuronal synaptic plasticity modulation of chemical synaptic transmission cell-cell signaling chemical synaptic transmission synaptic signaling regulation of trans-synaptic signaling anterograde trans-synaptic signaling regulation of cell communication cellular localization establishment of localization in cell intracellular transport endosomal transport biological process involved in interspecies interaction between organisms host-mediated perturbation of viral process modulation of process of another organism host-mediated perturbation of symbiont process regulation of localization regulated exocytosis synaptic vesicle cycle synaptic vesicle exocytosis vesicle-mediated transport in synapse regulation of regulated secretory pathway regulation of secretion by cell secretion by cell signal release neurotransmitter secretion regulation of transport secretion regulation of neurotransmitter transport regulation of synaptic vesicle exocytosis export from cell neurotransmitter transport regulation of vesicle-mediated transport regulation of secretion signal release from synapse exocytosis regulation of neurotransmitter secretion regulation of exocytosis synaptic vesicle recycling positive regulation of biological process positive regulation of secretion by cell positive regulation of exocytosis positive regulation of secretion positive regulation of cellular process positive regulation of transport establishment of protein localization protein transport intracellular protein transport multicellular organismal process amyloid-beta clearance amyloid-beta clearance by transcytosis transcytosis filopodium assembly plasma membrane bounded cell projection organization cell projection organization regulation of cell projection organization regulation of cell projection assembly regulation of filopodium assembly plasma membrane bounded cell projection assembly regulation of plasma membrane bounded cell projection assembly cell projection assembly regulation of plasma membrane bounded cell projection organization vesicle-mediated transport between endosomal compartments intercellular transport early endosome to late endosome transport	membrane-bounded organelle intracellular anatomical structure intracellular vesicle intracellular organelle cellular anatomical structure bounding membrane of organelle cytoplasmic vesicle vesicle membrane clathrin-coated vesicle endocytic vesicle membrane coated vesicle vesicle endocytic vesicle clathrin-coated vesicle membrane membrane-bounded organelle intracellular anatomical structure intracellular vesicle intracellular organelle cellular anatomical structure bounding membrane of organelle cytoplasmic vesicle vesicle membrane clathrin-coated vesicle endocytic vesicle membrane coated vesicle vesicle endocytic vesicle clathrin-coated vesicle membrane clathrin-coated endocytic vesicle membrane membrane intracellular membrane-bounded organelle clathrin-coated endocytic vesicle cytoplasmic vesicle membrane coated vesicle membrane organelle cytoplasm organelle membrane extracellular exosome extracellular vesicle extracellular organelle extracellular region extracellular membrane-bounded organelle cytoskeleton membraneless organelle intracellular membraneless organelle actin cytoskeleton cytosol somatodendritic compartment cell projection dendrite dendritic tree neuron projection plasma membrane bounded cell projection endosome membrane cytoplasmic side of membrane early endosome early endosome membrane endomembrane system cytoplasmic side of endosome membrane cytoplasmic side of early endosome membrane endosome side of membrane phagocytic vesicle phagocytic vesicle membrane ruffle cell leading edge cell body neuronal cell body synapse transport vesicle membrane presynapse synaptic vesicle synaptic vesicle membrane cell junction transport vesicle exocytic vesicle membrane secretory vesicle exocytic vesicle axon pigment granule melanosome axon terminus distal axon terminal bouton neuron projection terminus cell periphery plasma membrane membrane microdomain membrane raft early phagosome nucleus membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen
A, E	Rab5 GDP/GTP exchange factor	small GTPase binding protein binding binding enzyme binding GTPase binding aminoacyltransferase activity ubiquitin-like protein transferase activity catalytic activity, acting on a protein acyltransferase activity ubiquitin-like protein ligase activity ubiquitin protein ligase activity transferase activity catalytic activity ubiquitin-protein transferase activity small GTPase binding protein binding binding enzyme binding GTPase binding aminoacyltransferase activity ubiquitin-like protein transferase activity catalytic activity, acting on a protein acyltransferase activity ubiquitin-like protein ligase activity ubiquitin protein ligase activity transferase activity catalytic activity ubiquitin-protein transferase activity DNA binding nucleic acid binding GTPase regulator activity enzyme regulator activity guanyl-nucleotide exchange factor activity nucleoside-triphosphatase regulator activity molecular function regulator activity cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding	leukocyte migration immune system process mast cell migration myeloid leukocyte migration cell migration cellular process cell motility interleukin-6 production multicellular organismal process regulation of cellular process negative regulation of biological process regulation of interleukin-6 production regulation of cytokine production cytokine production leukocyte migration immune system process mast cell migration myeloid leukocyte migration cell migration cellular process cell motility interleukin-6 production multicellular organismal process regulation of cellular process negative regulation of biological process regulation of interleukin-6 production regulation of cytokine production cytokine production negative regulation of cellular process regulation of multicellular organismal process negative regulation of macromolecule metabolic process regulation of biosynthetic process regulation of biological process negative regulation of metabolic process biological regulation negative regulation of cytokine production regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulation of gene expression negative regulation of interleukin-6 production negative regulation of gene expression biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process regulation of macromolecule biosynthetic process metabolic process macromolecule metabolic process negative regulation of multicellular organismal process regulation of metabolic process localization establishment of protein localization protein transport transport macromolecule localization intracellular protein localization establishment of localization regulation of immune effector process response to stimulus negative regulation of mast cell cytokine production mast cell cytokine production regulation of immune system process myeloid leukocyte cytokine production cytokine production involved in immune response production of molecular mediator of immune response negative regulation of cytokine production involved in immune response regulation of cytokine production involved in immune response regulation of mast cell cytokine production immune response negative regulation of immune effector process immune effector process negative regulation of production of molecular mediator of immune response negative regulation of immune system process regulation of production of molecular mediator of immune response regulation of defense response regulation of response to external stimulus negative regulation of inflammatory response defense response negative regulation of response to stimulus response to external stimulus regulation of inflammatory response regulation of response to stimulus response to stress negative regulation of response to external stimulus regulation of response to stress negative regulation of defense response inflammatory response cellular response to stimulus small GTPase-mediated signal transduction signaling negative regulation of signaling regulation of small GTPase mediated signal transduction negative regulation of intracellular signal transduction regulation of signal transduction intracellular signal transduction negative regulation of cell communication cell communication regulation of intracellular signal transduction regulation of Ras protein signal transduction intracellular signaling cassette signal transduction regulation of signaling Ras protein signal transduction negative regulation of small GTPase mediated signal transduction negative regulation of signal transduction negative regulation of Ras protein signal transduction regulation of cell communication cellular localization establishment of protein localization to membrane protein targeting localization within membrane protein targeting to membrane intracellular transport dendritic transport axo-dendritic transport establishment of localization in cell microtubule-based transport transport along microtubule cytoskeleton-dependent intracellular transport microtubule-based movement microtubule-based process regulation of localization import into cell regulation of cellular component organization negative regulation of transport negative regulation of endocytosis vesicle-mediated transport cellular component organization cellular component organization or biogenesis regulation of endocytosis negative regulation of cellular component organization negative regulation of receptor-mediated endocytosis regulation of transport regulation of receptor-mediated endocytosis regulation of vesicle-mediated transport endocytosis receptor-mediated endocytosis endosomal transport establishment of organelle localization regulated exocytosis cell activation involved in immune response leukocyte degranulation myeloid leukocyte activation myeloid leukocyte mediated immunity leukocyte activation secretion by cell organelle localization leukocyte activation involved in immune response mast cell activation leukocyte mediated immunity mast cell mediated immunity secretion cell activation vacuolar localization export from cell mast cell degranulation myeloid cell activation involved in immune response mast cell activation involved in immune response exocytosis lysosome localization regulation of myeloid leukocyte mediated immunity negative regulation of secretion negative regulation of secretion by cell negative regulation of myeloid leukocyte mediated immunity regulation of secretion regulation of leukocyte mediated immunity negative regulation of regulated secretory pathway negative regulation of leukocyte degranulation regulation of mast cell degranulation regulation of regulated secretory pathway regulation of secretion by cell negative regulation of exocytosis negative regulation of mast cell degranulation regulation of leukocyte degranulation regulation of exocytosis negative regulation of leukocyte mediated immunity response to cytokine negative regulation of Kit signaling pathway cytokine-mediated signaling pathway cell surface receptor protein tyrosine kinase signaling pathway regulation of Kit signaling pathway cellular response to cytokine stimulus enzyme-linked receptor protein signaling pathway cell surface receptor signaling pathway regulation of cytokine-mediated signaling pathway cellular response to stem cell factor stimulus response to peptide regulation of response to cytokine stimulus negative regulation of response to cytokine stimulus Kit signaling pathway negative regulation of cytokine-mediated signaling pathway response to chemical response to stem cell factor immune response-regulating cell surface receptor signaling pathway positive regulation of biological process positive regulation of response to stimulus regulation of Fc receptor mediated stimulatory signaling pathway immune response-activating signaling pathway immune response-regulating signaling pathway positive regulation of immune response positive regulation of immune system process immune response-activating cell surface receptor signaling pathway Fc receptor mediated stimulatory signaling pathway regulation of immune response activation of immune response negative regulation of locomotion regulation of cell motility regulation of leukocyte migration negative regulation of leukocyte migration regulation of locomotion regulation of cell migration negative regulation of cell motility negative regulation of cell migration locomotion regulation of leukocyte activation regulation of cell activation negative regulation of cell activation negative regulation of mast cell activation regulation of mast cell activation negative regulation of leukocyte activation	membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle nucleolus intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle membraneless organelle nuclear lumen membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle nucleolus intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle membraneless organelle nuclear lumen cytoplasm cytosol somatodendritic compartment cell projection dendrite dendritic tree neuron projection plasma membrane bounded cell projection intracellular vesicle cytoplasmic vesicle vesicle endocytic vesicle early endosome endosome endomembrane system endosome membrane membrane early endosome membrane cytoplasmic vesicle membrane bounding membrane of organelle vesicle membrane organelle membrane recycling endosome synapse presynapse cell junction presynaptic endosome

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C, D, G, H	IPR003914	Rabaptin	Family
C, D, G, H	IPR015390	Rabaptin, GTPase-Rab5 binding domain	Domain
C, D, G, H	IPR018514	Rabaptin coiled-coil domain	Domain
B, F	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
B, F	IPR005225	Small GTP-binding domain	Domain
B, F	IPR001806	Small GTPase	Family
A, E	IPR002653	Zinc finger, A20-type	Domain
A, E	IPR045046	Vacuolar protein sorting-associated protein 9-like	Family
A, E	IPR003123	VPS9 domain	Domain
A, E	IPR041545	RABX5, catalytic core helical domain	Domain
A, E	IPR037191	VPS9 domain superfamily	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
C, D, G, H	: Q15276	rheumatoid arthritis breast cancer hereditary spastic paraplegia ovarian cancer psoriasis Gaucher disease malignant glioma pancreatic ductal adenocarcinoma glioblastoma osteosarcoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia
B, F	: P20339	adenoma large cell medulloblastoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia subependymal giant cell astrocytoma coronary artery disease myocardial ischemia pilocytic astrocytoma Gaucher disease osteosarcoma psoriasis

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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.