1TU3

Crystal Structure of Rab5 complex with Rabaptin5 C-terminal Domain

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
Pharos: Disease Associations

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d1tu3a_	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	G proteins	Rab5a	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d1tu3b_	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	G proteins	Rab5a	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d1tu3c_	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	G proteins	Rab5a	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D	d1tu3d_	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	G proteins	Rab5a	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
E	d1tu3e_	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	G proteins	Rab5a	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
F	d1tu3f_	Coiled coil proteins	Parallel coiled-coil	G protein-binding domain	Rabaptin-5	Rabaptin-5	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
G	d1tu3g_	Coiled coil proteins	Parallel coiled-coil	G protein-binding domain	Rabaptin-5	Rabaptin-5	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
H	d1tu3h_	Coiled coil proteins	Parallel coiled-coil	G protein-binding domain	Rabaptin-5	Rabaptin-5	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
I	d1tu3i_	Coiled coil proteins	Parallel coiled-coil	G protein-binding domain	Rabaptin-5	Rabaptin-5	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
J	d1tu3j_	Coiled coil proteins	Parallel coiled-coil	G protein-binding domain	Rabaptin-5	Rabaptin-5	human (Homo sapiens ) [TaxId: 9606 ],	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	8054292	3002022	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Ras-like P-loop GTPases	8054292	3002022	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Ras-like P-loop GTPases	8054292	3002022	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Ras-like P-loop GTPases	8054292	3002022	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Ras-like P-loop GTPases	8054292	3002022	SCOP2B (2022-06-29)
F	SCOP2 Family	Rabaptin-5	8030262	4003962	SCOP2 (2022-06-29)
F	SCOP2 Superfamily	G protein-binding domain	8042641	3000514	SCOP2 (2022-06-29)
G	SCOP2B Superfamily	G protein-binding domain	8042641	3000514	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	G protein-binding domain	8042641	3000514	SCOP2B (2022-06-29)
I	SCOP2B Superfamily	G protein-binding domain	8042641	3000514	SCOP2B (2022-06-29)
J	SCOP2B Superfamily	G protein-binding domain	8042641	3000514	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	e1tu3A1	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)
B	Ras	e1tu3B1	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	e1tu3C1	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)
D	Ras	e1tu3D1	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)
E	Ras	e1tu3E1	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)
B	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)
D	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
E	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
F	1.20.5.730	Mainly Alpha	Up-down Bundle	Single alpha-helices involved in coiled-coils or other helix-helix interfaces	Single helix bin	CATH (4.3.0)
G	1.20.5.730	Mainly Alpha	Up-down Bundle	Single alpha-helices involved in coiled-coils or other helix-helix interfaces	Single helix bin	CATH (4.3.0)
H	1.20.5.730	Mainly Alpha	Up-down Bundle	Single alpha-helices involved in coiled-coils or other helix-helix interfaces	Single helix bin	CATH (4.3.0)
I	1.20.5.730	Mainly Alpha	Up-down Bundle	Single alpha-helices involved in coiled-coils or other helix-helix interfaces	Single helix bin	CATH (4.3.0)
J	1.20.5.730	Mainly Alpha	Up-down Bundle	Single alpha-helices involved in coiled-coils or other helix-helix interfaces	Single helix bin	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, E	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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D, E	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 organic cyclic compound 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 import into cell receptor internalization transport receptor-mediated endocytosis 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 import into cell receptor internalization transport receptor-mediated endocytosis endocytosis establishment of localization vesicle-mediated transport 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 catabolic process cellular component assembly process utilizing autophagic mechanism autophagosome assembly organelle assembly vacuole organization cellular metabolic process 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 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 regulation of localization cellular 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 establishment of localization in cell 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 modulation by host of viral process biological process involved in interspecies interaction between organisms modulation by host of symbiont process biological process involved in interaction with symbiont biological process involved in symbiotic interaction protein localization establishment of protein localization nitrogen compound transport intracellular transport protein transport cellular macromolecule localization macromolecule localization 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 endosomal transport vesicle-mediated transport between endosomal compartments early endosome to late endosome transport	membrane-bounded organelle intracellular anatomical structure intracellular vesicle intracellular organelle 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-bounded organelle intracellular anatomical structure intracellular vesicle intracellular organelle 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 cellular anatomical entity 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 space extracellular membrane-bounded organelle cytoskeleton intracellular non-membrane-bounded organelle actin cytoskeleton non-membrane-bounded organelle 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 postsynaptic early endosome synapse postsynaptic endosome postsynapse cell junction ruffle cell leading edge cell body neuronal cell body transport vesicle membrane presynapse synaptic vesicle synaptic vesicle membrane 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
F, G, H, I, J	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 signaling receptor binding molecular function regulator activity signaling receptor regulator activity growth factor activity receptor ligand activity signaling receptor activator activity GTPase regulator activity protein binding binding protein domain specific binding identical protein binding protein homodimerization activity protein dimerization activity molecular function activator activity signaling receptor binding 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 protein localization establishment of protein localization nitrogen compound transport protein transport cellular macromolecule localization macromolecule 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	membrane-bounded organelle intracellular anatomical structure early endosome endosome intracellular vesicle cellular anatomical entity intracellular membrane-bounded organelle endomembrane system intracellular organelle cytoplasmic vesicle organelle cytoplasm vesicle endosome membrane membrane-bounded organelle intracellular anatomical structure early endosome endosome intracellular vesicle cellular anatomical entity intracellular membrane-bounded organelle endomembrane system intracellular organelle cytoplasmic vesicle organelle cytoplasm vesicle endosome membrane membrane early endosome membrane cytoplasmic vesicle membrane bounding membrane of organelle vesicle membrane organelle membrane recycling endosome endocytic vesicle protein-containing complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
A, B, C, D, E	IPR005225	Small GTP-binding domain	Domain
A, B, C, D, E	IPR001806	Small GTPase	Family
F, G, H, I, J	IPR003914	Rabaptin	Family
F, G, H, I, J	IPR015390	Rabaptin, GTPase-Rab5 binding domain	Domain
F, G, H, I, J	IPR018514	Rabaptin coiled-coil domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B, C, D, E	Pharos: 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
F, G, H, I, J	Pharos: 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

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.