4UJ4

Crystal structure of human Rab11-Rabin8-FIP3

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)
A	SCOP2B Superfamily	Ras-like P-loop GTPases	8057254	3002022	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Ras-like P-loop GTPases	8057254	3002022	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	Ras-like P-loop GTPases	8057254	3002022	SCOP2B (2022-06-29)
J	SCOP2B Superfamily	Ras-like P-loop GTPases	8057254	3002022	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Eferin C-derminal domain-like	8039617	3000568	SCOP2B (2022-06-29)
I	SCOP2B Superfamily	Eferin C-derminal domain-like	8039617	3000568	SCOP2B (2022-06-29)
L	SCOP2B Superfamily	Eferin C-derminal domain-like	8039617	3000568	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	e4uj4A1	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	e4uj4D1	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)
G	Ras	e4uj4G1	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)
J	Ras	e4uj4J1	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	KOG4324	e4uj4B1	A: alpha bundles	X: Rabin8 C-terminal domain (From Topology)	H: Rabin8 C-terminal domain (From Topology)	T: Rabin8 C-terminal domain	F: KOG4324	ECOD (1.6)
E	KOG4324	e4uj4E1	A: alpha bundles	X: Rabin8 C-terminal domain (From Topology)	H: Rabin8 C-terminal domain (From Topology)	T: Rabin8 C-terminal domain	F: KOG4324	ECOD (1.6)
H	KOG4324	e4uj4H1	A: alpha bundles	X: Rabin8 C-terminal domain (From Topology)	H: Rabin8 C-terminal domain (From Topology)	T: Rabin8 C-terminal domain	F: KOG4324	ECOD (1.6)
K	KOG4324	e4uj4K1	A: alpha bundles	X: Rabin8 C-terminal domain (From Topology)	H: Rabin8 C-terminal domain (From Topology)	T: Rabin8 C-terminal domain	F: KOG4324	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, D, G, J	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
C, F, I, L	PF09457	FIP domain (RBD-FIP)	FIP domain	-	Motif

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, D, G, J	Ras-related protein Rab-11A	protein binding binding SNARE binding syntaxin binding cytoskeletal protein binding microtubule binding tubulin binding dynein light intermediate chain 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 protein binding binding SNARE binding syntaxin binding cytoskeletal protein binding microtubule binding tubulin binding dynein light intermediate chain 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 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 myosin V binding myosin binding G protein activity molecular function regulator activity	regulation of localization regulation of biological process cellular localization regulation of cellular process regulation of transport transport biological regulation intracellular transport localization within membrane regulation of vesicle-mediated transport establishment of localization vesicle-mediated transport endocytic recycling endosomal transport vesicle-mediated transport to the plasma membrane regulation of localization regulation of biological process cellular localization regulation of cellular process regulation of transport transport biological regulation intracellular transport localization within membrane regulation of vesicle-mediated transport establishment of localization vesicle-mediated transport endocytic recycling endosomal transport vesicle-mediated transport to the plasma membrane localization regulation of cellular localization establishment of localization in cell cellular process regulation of endocytic recycling regulation of intracellular transport cellular component organization regulation of cellular component size regulation of vesicle size regulation of multivesicular body size cellular component organization or biogenesis regulation of biological quality regulation of endosome size regulation of anatomical structure size plasma membrane to endosome transport establishment of organelle localization mitotic metaphase chromosome alignment mitotic cell cycle metaphase chromosome alignment chromosome localization organelle localization mitotic sister chromatid segregation cell cycle chromosome segregation cell cycle process mitotic nuclear division organelle fission chromosome organization sister chromatid segregation organelle organization nuclear division mitotic cell cycle process nuclear chromosome segregation establishment of chromosome localization protein localization protein localization to cell periphery protein localization to plasma membrane cellular macromolecule localization macromolecule localization protein localization to membrane regulation of cytokinesis regulation of cell cycle process cytokinesis regulation of cell division cell division regulation of cell cycle vesicle localization establishment of melanosome localization establishment of vesicle localization cellular pigmentation pigment granule transport establishment of pigment granule localization pigmentation pigment granule localization melanosome transport melanosome localization regulation of cellular component organization cell projection organization plasma membrane bounded cell projection assembly cellular component biogenesis cellular component assembly cilium assembly cilium organization organelle assembly plasma membrane bounded cell projection organization regulation of cell projection organization regulation of cell projection assembly regulation of cellular component biogenesis regulation of organelle organization regulation of plasma membrane bounded cell projection assembly regulation of cilium assembly regulation of organelle assembly cell projection assembly regulation of plasma membrane bounded cell projection organization protein localization to microtubule cytoskeleton regulation of protein localization regulation of protein localization to centrosome protein localization to microtubule organizing center protein localization to cytoskeleton protein localization to organelle protein localization to centrosome developmental process multicellular organismal process cellular developmental process cell development neuron projection development nervous system development generation of neurons neurogenesis multicellular organism development neuron differentiation cell differentiation neuron development anatomical structure development system development protein localization to cilium multivesicular body assembly vesicle organization multivesicular body organization endosome organization endomembrane system organization protein localization to cell surface microtubule cytoskeleton organization astral microtubule organization cytoplasmic microtubule organization microtubule-based process supramolecular fiber organization cytoskeleton organization spindle organization non-membrane-bounded organelle assembly microtubule cytoskeleton organization involved in mitosis spindle assembly mitotic spindle organization mitotic spindle assembly establishment of protein localization establishment of protein localization to membrane establishment of protein localization to organelle amyloid-beta clearance amyloid-beta clearance by transcytosis transcytosis secretion by cell exocytosis secretion export from cell exosomal secretion extracellular exosome biogenesis extracellular vesicle biogenesis vesicle-mediated transport between endosomal compartments early endosome to recycling endosome transport regulation of early endosome to recycling endosome transport nitrogen compound transport protein localization to synapse neurotransmitter receptor transport to postsynaptic membrane establishment of protein localization to plasma membrane establishment of protein localization to postsynaptic membrane neurotransmitter receptor transport to plasma membrane neurotransmitter receptor transport, endosome to plasma membrane neurotransmitter receptor transport, endosome to postsynaptic membrane protein localization to postsynaptic membrane neurotransmitter receptor transport organic substance transport protein-containing complex localization endosome to plasma membrane protein transport regulation of postsynaptic membrane neurotransmitter receptor levels protein transport protein localization to postsynapse protein localization to cell junction receptor localization to synapse intracellular protein transport regulation of cell cycle phase transition G2/M transition of mitotic cell cycle positive regulation of biological process cell cycle phase transition regulation of mitotic cell cycle positive regulation of mitotic cell cycle phase transition positive regulation of cell cycle process positive regulation of mitotic cell cycle positive regulation of cellular process cell cycle G2/M phase transition positive regulation of G2/M transition of mitotic cell cycle regulation of G2/M transition of mitotic cell cycle regulation of cell cycle G2/M phase transition positive regulation of cell cycle G2/M phase transition positive regulation of cell cycle regulation of mitotic cell cycle phase transition positive regulation of cell cycle phase transition mitotic cell cycle phase transition positive regulation of locomotion regulation of cell motility positive regulation of cell migration positive regulation of epithelial cell migration tissue migration ameboidal-type cell migration positive regulation of cell motility regulation of cell migration cell migration regulation of multicellular organismal process epithelial cell migration cell motility regulation of epithelial cell migration locomotion epithelium migration regulation of locomotion	intracellular organelle intracellular anatomical structure cytoskeleton spindle organelle intracellular non-membrane-bounded organelle spindle pole cellular anatomical entity microtubule cytoskeleton non-membrane-bounded organelle extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle intracellular organelle intracellular anatomical structure cytoskeleton spindle organelle intracellular non-membrane-bounded organelle spindle pole cellular anatomical entity microtubule cytoskeleton non-membrane-bounded organelle extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region extracellular space vesicle extracellular membrane-bounded organelle cytoplasm cytosol synapse cell junction glutamatergic synapse membrane intracellular vesicle intracellular membrane-bounded organelle cytoplasmic vesicle membrane bounding membrane of organelle cytoplasmic vesicle vesicle membrane endocytic vesicle membrane organelle membrane endocytic vesicle Golgi apparatus subcompartment Golgi apparatus organelle subcompartment endomembrane system trans-Golgi network Golgi membrane endosome recycling endosome centrosome microtubule organizing center centriolar satellite centriole phagocytic vesicle transport vesicle cell division site cell periphery cleavage furrow plasma membrane plasma membrane region late endosome multivesicular body protein-containing complex endosome membrane recycling endosome membrane postsynaptic recycling endosome postsynaptic endosome postsynapse trans-Golgi network membrane
B, E, H, K	Rab-3A-interacting protein	GTPase regulator activity enzyme regulator activity guanyl-nucleotide exchange factor activity nucleoside-triphosphatase regulator activity molecular function regulator activity protein binding binding enzyme binding GTPase binding identical protein binding	filopodium assembly regulation of cellular component organization regulation of cellular process cell projection organization negative regulation of filopodium assembly negative regulation of biological process regulation of filopodium assembly plasma membrane bounded cell projection assembly cellular component organization cellular component biogenesis negative regulation of plasma membrane bounded cell projection assembly cellular component assembly negative regulation of cellular process cellular component organization or biogenesis filopodium assembly regulation of cellular component organization regulation of cellular process cell projection organization negative regulation of filopodium assembly negative regulation of biological process regulation of filopodium assembly plasma membrane bounded cell projection assembly cellular component organization cellular component biogenesis negative regulation of plasma membrane bounded cell projection assembly cellular component assembly negative regulation of cellular process cellular component organization or biogenesis negative regulation of cell projection organization regulation of biological process plasma membrane bounded cell projection organization negative regulation of cellular component organization regulation of cell projection organization regulation of cell projection assembly biological regulation regulation of cellular component biogenesis regulation of plasma membrane bounded cell projection assembly cellular process cell projection assembly regulation of plasma membrane bounded cell projection organization 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 ciliary basal body-plasma membrane docking organelle assembly membrane docking organelle localization by membrane tethering organelle organization organelle localization cilium assembly cilium organization protein localization establishment of protein localization nitrogen compound transport organic substance transport protein transport cellular macromolecule localization macromolecule localization protein localization to organelle secretion by cell exocytosis secretion export from cell establishment of protein localization to membrane protein targeting protein localization to membrane protein targeting to membrane	membrane-bounded organelle intracellular anatomical structure transport vesicle intracellular vesicle cellular anatomical entity intracellular membrane-bounded organelle endomembrane system intracellular organelle cytoplasmic vesicle Golgi to plasma membrane transport vesicle organelle secretory vesicle cytoplasm vesicle membrane-bounded organelle intracellular anatomical structure transport vesicle intracellular vesicle cellular anatomical entity intracellular membrane-bounded organelle endomembrane system intracellular organelle cytoplasmic vesicle Golgi to plasma membrane transport vesicle organelle secretory vesicle cytoplasm vesicle exocytic vesicle cell projection cell leading edge plasma membrane bounded cell projection lamellipodium somatodendritic compartment proximal dendrite dendrite dendritic tree neuron projection centrosome microtubule organizing center cytoskeleton intracellular non-membrane-bounded organelle microtubule cytoskeleton non-membrane-bounded organelle cytosol perinuclear region of cytoplasm cilium ciliary basal body nucleus
C, F, I, L	Rab11 family-interacting protein 3	small GTPase binding protein binding binding enzyme binding GTPase binding cation binding ion binding calcium ion binding metal ion binding small molecule binding identical protein binding protein homodimerization activity protein dimerization activity protein-containing complex binding small GTPase binding protein binding binding enzyme binding GTPase binding cation binding ion binding calcium ion binding metal ion binding small molecule binding identical protein binding protein homodimerization activity protein dimerization activity protein-containing complex binding dynein light intermediate chain binding molecular adaptor activity	protein localization localization cellular localization protein localization to cilium protein localization to organelle cellular macromolecule localization macromolecule localization cellular process regulation of localization regulation of biological process regulation of cellular process regulation of transport transport biological regulation protein localization localization cellular localization protein localization to cilium protein localization to organelle cellular macromolecule localization macromolecule localization cellular process regulation of localization regulation of biological process regulation of cellular process regulation of transport transport biological regulation intracellular transport localization within membrane regulation of vesicle-mediated transport establishment of localization vesicle-mediated transport endocytic recycling endosomal transport vesicle-mediated transport to the plasma membrane regulation of cellular localization establishment of localization in cell regulation of endocytic recycling regulation of intracellular transport cell division negative regulation of protein transport multicellular organismal process establishment of protein localization system process nitrogen compound transport negative regulation of adiponectin secretion negative regulation of biological process regulation of adiponectin secretion negative regulation of transport cell communication adiponectin secretion negative regulation of secretion negative regulation of hormone secretion negative regulation of secretion by cell regulation of biological quality regulation of hormone levels organic substance transport establishment of protein localization to extracellular region negative regulation of establishment of protein localization protein secretion regulation of protein secretion regulation of secretion endocrine hormone secretion negative regulation of protein secretion negative regulation of multicellular organismal process regulation of hormone secretion regulation of protein localization signaling negative regulation of signaling hormone secretion negative regulation of cell communication protein localization to extracellular region secretion by cell regulation of secretion by cell signal release negative regulation of cellular process regulation of multicellular organismal process negative regulation of protein localization regulation of signaling secretion regulation of establishment of protein localization export from cell cell-cell signaling regulation of protein transport endocrine process protein transport hormone transport regulation of cell communication cell cycle regulation of cytokinesis regulation of cell cycle process cytokinesis regulation of cell division regulation of cell cycle cell cycle process regulation of cellular component organization cell projection organization plasma membrane bounded cell projection assembly cellular component biogenesis cellular component organization cellular component assembly cilium assembly cellular component organization or biogenesis cilium organization organelle assembly plasma membrane bounded cell projection organization regulation of cell projection organization regulation of cell projection assembly regulation of cellular component biogenesis regulation of organelle organization regulation of plasma membrane bounded cell projection assembly regulation of cilium assembly organelle organization regulation of organelle assembly cell projection assembly regulation of plasma membrane bounded cell projection organization protein localization to microtubule cytoskeleton regulation of protein localization to centrosome protein localization to microtubule organizing center protein localization to cytoskeleton protein localization to centrosome vesicle-mediated transport between endosomal compartments early endosome to recycling endosome transport regulation of early endosome to recycling endosome transport	membrane-bounded organelle intracellular organelle intracellular anatomical structure mitochondrion organelle cytoplasm cellular anatomical entity intracellular membrane-bounded organelle midbody centrosome microtubule organizing center cytoskeleton intracellular non-membrane-bounded organelle microtubule cytoskeleton membrane-bounded organelle intracellular organelle intracellular anatomical structure mitochondrion organelle cytoplasm cellular anatomical entity intracellular membrane-bounded organelle midbody centrosome microtubule organizing center cytoskeleton intracellular non-membrane-bounded organelle microtubule cytoskeleton non-membrane-bounded organelle centriolar satellite cytosol intracellular vesicle cytoplasmic vesicle vesicle endocytic vesicle cell division site cell periphery cleavage furrow membrane plasma membrane plasma membrane region nucleus membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen cytoplasmic vesicle membrane bounding membrane of organelle vesicle membrane endocytic vesicle membrane organelle membrane intercellular bridge endosome membrane endosome recycling endosome endomembrane system recycling endosome membrane Golgi membrane Golgi apparatus synapse postsynaptic recycling endosome postsynaptic endosome cell junction postsynapse postsynaptic recycling endosome membrane postsynaptic endosome membrane Golgi apparatus subcompartment organelle subcompartment trans-Golgi network membrane trans-Golgi network

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, D, G, J	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
A, D, G, J	IPR001806	Small GTPase	Family
A, D, G, J	IPR005225	Small GTP-binding protein domain	Domain
B, E, H, K	IPR009449	GDP/GTP exchange factor Sec2, N-terminal	Domain
B, E, H, K	IPR040351	Guanine nucleotide exchange factor RAB3IL/RAB3IP/Sec2	Family
C, F, I, L	IPR037245	FIP-RBD, C-terminal domain superfamily	Homologous Superfamily
C, F, I, L	IPR002048	EF-hand domain	Domain
C, F, I, L	IPR011992	EF-hand domain pair	Homologous Superfamily
C, F, I, L	IPR019018	Rab-binding domain FIP-RBD	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, D, G, J	Pharos: P62491	Chloracne interstitial cystitis malignant pancreatic neoplasm ovarian cancer Pick disease dermatomyositis large cell medulloblastoma myopathy pancreatic ductal adenocarcinoma plasma cell myeloma Hodgkins lymphoma lymphoplasmacytic lymphoma non-small cell lung carcinoma pancreatic intraductal papillary-mucinous neoplasm psoriasis
B, E, H, K	Pharos: Q96QF0	atrial fibrillation breast carcinoma gastric cancer large cell medulloblastoma medulloblastoma ovarian cancer pituitary cancer atypical teratoid rhabdoid tumor Crohn disease gastric carcinoma lung carcinoma oligodendroglioma pancreatic intraductal papillary-mucinous neoplasm ulcerative colitis breast cancer atrial fibrillation breast carcinoma gastric cancer large cell medulloblastoma medulloblastoma ovarian cancer pituitary cancer atypical teratoid rhabdoid tumor Crohn disease gastric carcinoma lung carcinoma oligodendroglioma pancreatic intraductal papillary-mucinous neoplasm ulcerative colitis breast cancer ductal breast carcinoma in situ invasive ductal breast carcinoma malignant ependymoma osteosarcoma pilocytic astrocytoma
C, F, I, L	Pharos: O75154	Sjogren syndrome adrenal cortex adenoma atypical teratoid rhabdoid tumor Hodgkins lymphoma malignant ependymoma myopathy osteoporosis Pick disease amyotrophic lateral sclerosis gastric carcinoma juvenile dermatomyositis malignant glioma nephrosclerosis ovarian cancer progressive supranuclear palsy Sjogren syndrome adrenal cortex adenoma atypical teratoid rhabdoid tumor Hodgkins lymphoma malignant ependymoma myopathy osteoporosis Pick disease amyotrophic lateral sclerosis gastric carcinoma juvenile dermatomyositis malignant glioma nephrosclerosis ovarian cancer progressive supranuclear palsy astrocytic tumor glioblastoma large cell medulloblastoma medulloblastoma oligodendroglioma pancreatic ductal adenocarcinoma

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.