2D7C

Crystal structure of human Rab11 in complex with FIP3 Rab-binding 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	d2d7ca_	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	G proteins	Rab11a	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d2d7cb_	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	G proteins	Rab11a	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D	d2d7cd_	Coiled coil proteins	Parallel coiled-coil	Eferin C-derminal domain-like	Eferin C-derminal domain-like	Rab11 family-interacting protein 3 (Rab11-FIP3, Eferin)	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d2d7cc1	Coiled coil proteins	Parallel coiled-coil	Eferin C-derminal domain-like	Eferin C-derminal domain-like	Rab11 family-interacting protein 3 (Rab11-FIP3, Eferin)	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	8057254	3002022	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Ras-like P-loop GTPases	8057254	3002022	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Eferin C-derminal domain-like	8039617	3000568	SCOP2B (2022-06-29)
C	SCOP2 Family	FIP domain-like	8027238	4000554	SCOP2 (2022-06-29)
C	SCOP2 Superfamily	Eferin C-derminal domain-like	8039617	3000568	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)
A	Ras	e2d7cA1	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	e2d7cB1	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)
D	1.20.5.2440	Mainly Alpha	Up-down Bundle	Single alpha-helices involved in coiled-coils or other helix-helix interfaces		CATH (4.3.0)
C	1.20.5.2440	Mainly Alpha	Up-down Bundle	Single alpha-helices involved in coiled-coils or other helix-helix interfaces		CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	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, D	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, B	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	protein localization Golgi to plasma membrane transport establishment of protein localization cellular localization nitrogen compound transport post-Golgi vesicle-mediated transport transport establishment of protein localization to plasma membrane Golgi to plasma membrane protein transport vesicle-mediated transport localization cellular macromolecule localization protein localization to cell periphery establishment of protein localization to membrane protein localization Golgi to plasma membrane transport establishment of protein localization cellular localization nitrogen compound transport post-Golgi vesicle-mediated transport transport establishment of protein localization to plasma membrane Golgi to plasma membrane protein transport vesicle-mediated transport localization 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 establishment of localization vesicle-mediated transport to the plasma membrane protein transport macromolecule localization cellular process Golgi vesicle transport regulation of localization regulation of biological process regulation of cellular process regulation of transport biological regulation intracellular transport regulation of vesicle-mediated transport endocytic recycling endosomal transport regulation of cellular localization establishment of localization in cell regulation of endocytic recycling regulation of intracellular transport plasma membrane to endosome transport establishment of organelle localization mitotic metaphase chromosome alignment mitotic cell cycle metaphase chromosome alignment cellular component organization chromosome localization organelle localization mitotic sister chromatid segregation cell cycle cellular component organization or biogenesis 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 regulation of cytokinesis regulation of cell cycle process cytokinesis regulation of cell division cell division regulation of cell cycle transmembrane transport protein transmembrane transport 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 vesicle-mediated transport between endosomal compartments early endosome to recycling endosome transport 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 positive regulation of cell division cytoskeleton-dependent cytokinesis regulation of mitotic cytokinetic process positive regulation of mitotic cytokinesis positive regulation of biological process mitotic cytokinetic process mitotic cytokinesis regulation of mitotic cytokinesis positive regulation of cytokinesis positive regulation of mitotic cytokinetic process positive regulation of cell cycle process positive regulation of cellular process regulation of cytokinetic process positive regulation of cell cycle cytokinetic process microtubule cytoskeleton organization astral microtubule organization cytoplasmic microtubule organization microtubule-based process supramolecular fiber organization cytoskeleton organization spindle organization membraneless organelle assembly microtubule cytoskeleton organization involved in mitosis spindle assembly mitotic spindle organization mitotic spindle assembly 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 regulation of early endosome to recycling endosome transport protein localization to synapse neurotransmitter receptor transport to postsynaptic membrane establishment of protein localization to postsynaptic membrane neurotransmitter receptor transport to plasma membrane neurotransmitter receptor transport, endosome to plasma membrane regulation of biological quality neurotransmitter receptor transport, endosome to postsynaptic membrane protein localization to postsynaptic membrane neurotransmitter receptor transport protein-containing complex localization endosome to plasma membrane protein transport regulation of postsynaptic membrane neurotransmitter receptor levels 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 cell cycle phase transition regulation of mitotic cell cycle positive regulation of mitotic cell cycle phase transition positive regulation of mitotic cell cycle 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 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 cellular anatomical structure intracellular anatomical structure cytoskeleton spindle organelle membraneless organelle intracellular membraneless organelle spindle pole microtubule cytoskeleton extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle intracellular organelle cellular anatomical structure intracellular anatomical structure cytoskeleton spindle organelle membraneless organelle intracellular membraneless organelle spindle pole microtubule cytoskeleton 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
C, D	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 protein-macromolecule adaptor activity molecular adaptor activity identical protein binding protein homodimerization activity small GTPase binding protein binding binding enzyme binding GTPase binding cation binding ion binding calcium ion binding metal ion binding small molecule binding protein-macromolecule adaptor activity molecular adaptor activity identical protein binding protein homodimerization activity protein dimerization activity protein-containing complex binding dynein light intermediate chain binding	protein localization Golgi to plasma membrane transport establishment of protein localization cellular localization nitrogen compound transport post-Golgi vesicle-mediated transport transport establishment of protein localization to plasma membrane Golgi to plasma membrane protein transport vesicle-mediated transport localization cellular macromolecule localization protein localization to cell periphery establishment of protein localization to membrane protein localization Golgi to plasma membrane transport establishment of protein localization cellular localization nitrogen compound transport post-Golgi vesicle-mediated transport transport establishment of protein localization to plasma membrane Golgi to plasma membrane protein transport vesicle-mediated transport localization 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 establishment of localization vesicle-mediated transport to the plasma membrane protein transport macromolecule localization cellular process Golgi vesicle transport protein localization to cilium protein localization to organelle regulation of localization regulation of biological process regulation of cellular process regulation of transport biological regulation intracellular transport regulation of vesicle-mediated transport endocytic recycling endosomal transport regulation of cellular localization establishment of localization in cell regulation of endocytic recycling regulation of intracellular transport cell division positive regulation of cell division cytoskeleton-dependent cytokinesis regulation of mitotic cytokinetic process positive regulation of mitotic cytokinesis positive regulation of biological process mitotic cytokinetic process mitotic cytokinesis mitotic cell cycle regulation of cell division regulation of mitotic cytokinesis positive regulation of cytokinesis positive regulation of mitotic cytokinetic process positive regulation of cell cycle process cell cycle regulation of cell cycle positive regulation of cellular process cell cycle process regulation of cytokinesis regulation of cell cycle process cytokinesis regulation of cytokinetic process positive regulation of cell cycle mitotic cell cycle process cytokinetic process negative regulation of protein transport multicellular organismal process system process 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 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 hormone transport regulation of cell communication protein localization to cell division site protein localization to cleavage furrow 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 positive regulation of organelle organization positive regulation of cellular component organization positive regulation of cell projection organization positive regulation of cellular component biogenesis positive regulation of cilium assembly positive regulation of plasma membrane bounded cell projection assembly positive regulation of organelle assembly 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 cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle midbody centrosome microtubule organizing center cytoskeleton membraneless organelle intracellular membraneless organelle membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle midbody centrosome microtubule organizing center cytoskeleton membraneless organelle intracellular membraneless organelle microtubule cytoskeleton 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, B	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
A, B	IPR005225	Small GTP-binding domain	Domain
A, B	IPR001806	Small GTPase	Family
A, B	IPR050209	Rab GTPases family involved in membrane trafficking	Family
C, D	IPR037245	FIP-RBD, C-terminal domain superfamily	Homologous Superfamily
C, D	IPR002048	EF-hand domain	Domain
C, D	IPR011992	EF-hand domain pair	Homologous Superfamily
C, D	IPR051977	Rab11-interacting regulator of endocytosis and ciliogenesis	Family
C, D	IPR019018	Rab-binding domain FIP-RBD	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B	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
C, D	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 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.