4LWZ

Crystal structure of Myo5b globular tail domain in complex with inactive Rab11a

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	d4lwza_	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	G proteins	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d4lwzc_	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	G proteins	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D	d4lwzd1	All alpha proteins	alpha-alpha superhelix	DIL domain-like	DIL domains from class V myosins	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D	d4lwzd2	Artifacts	Tags	Tags	Tags	N-terminal Tags	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d4lwzb_	All alpha proteins	alpha-alpha superhelix	DIL domain-like	DIL domains from class V myosins	automated matches	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)
C	SCOP2B Superfamily	Ras-like P-loop GTPases	8057254	3002022	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	e4lwzA1	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	e4lwzC1	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	DIL	e4lwzD1	A: alpha superhelices	X: Repetitive alpha hairpins	H: ARM repeat (From Topology)	T: ARM repeat	F: DIL	ECOD (1.6)
B	DIL	e4lwzB1	A: alpha superhelices	X: Repetitive alpha hairpins	H: ARM repeat (From Topology)	T: ARM repeat	F: DIL	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)
C	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, C	PF00071	Ras family (Ras)	Ras family	Includes sub-families Ras, Rab, Rac, Ral, Ran, Rap Ypt1 and more. Shares P-loop motif with GTP_EFTU, arf and myosin_head. See Pfam:PF00009 Pfam:PF00025, Pfam:PF00063. As regards Rab GTPases, these are important regulators of vesicle formation, motil ...	Includes sub-families Ras, Rab, Rac, Ral, Ran, Rap Ypt1 and more. Shares P-loop motif with GTP_EFTU, arf and myosin_head. See Pfam:PF00009 Pfam:PF00025, Pfam:PF00063. As regards Rab GTPases, these are important regulators of vesicle formation, motility and fusion. They share a fold in common with all Ras GTPases: this is a six-stranded beta-sheet surrounded by five alpha-helices [1].	Domain
B, D	PF01843	DIL domain (DIL)	DIL domain	-	Repeat

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, C	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 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 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 non-membrane-bounded 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 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 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, D	Unconventional myosin-Vb	small GTPase binding protein binding binding enzyme binding GTPase binding cytoskeletal protein binding actin binding protein-containing complex binding actin filament binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding small GTPase binding protein binding binding enzyme binding GTPase binding cytoskeletal protein binding actin binding protein-containing complex binding actin filament binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding calmodulin binding cytoskeletal motor activity microfilament motor activity ATP-dependent activity	protein localization establishment of protein localization cellular localization nitrogen compound transport transport establishment of localization localization protein transport cellular macromolecule localization macromolecule localization cellular process establishment of localization in cell intracellular transport vesicle-mediated transport protein localization establishment of protein localization cellular localization nitrogen compound transport transport establishment of localization localization protein transport cellular macromolecule localization macromolecule localization cellular process establishment of localization in cell intracellular transport vesicle-mediated transport endosomal transport vesicle transport along actin filament vesicle cytoskeletal trafficking vesicle localization establishment of organelle localization establishment of vesicle localization actin filament-based movement organelle localization actin filament-based process cytoskeleton-dependent intracellular transport actin filament-based transport cellular component organization organelle organization actin cytoskeleton organization actin filament organization cellular component organization or biogenesis supramolecular fiber organization cytoskeleton organization regulation of body fluid levels multicellular organismal process renal system process system process homeostatic process biological regulation multicellular organismal-level homeostasis chemical homeostasis multicellular organismal-level water homeostasis multicellular organismal-level chemical homeostasis renal water homeostasis regulation of biological quality	membrane cellular anatomical entity membrane-bounded organelle organelle vesicle extracellular exosome extracellular vesicle extracellular organelle extracellular region extracellular space extracellular membrane-bounded organelle intracellular organelle intracellular anatomical structure cytoskeleton membrane cellular anatomical entity membrane-bounded organelle organelle vesicle extracellular exosome extracellular vesicle extracellular organelle extracellular region extracellular space extracellular membrane-bounded organelle intracellular organelle intracellular anatomical structure cytoskeleton intracellular non-membrane-bounded organelle actin cytoskeleton non-membrane-bounded organelle cytoplasm protein-containing complex myosin complex intracellular vesicle intracellular membrane-bounded organelle cytoplasmic vesicle membrane vesicle membrane cytoplasmic vesicle organelle membrane cell periphery cell cortex apical part of cell cell cortex region cytoplasmic region apical cortex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, C	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
A, C	IPR005225	Small GTP-binding domain	Domain
A, C	IPR001806	Small GTPase	Family
A, C	IPR050209	Rab GTPases family involved in membrane trafficking	Family
B, D	IPR036961	Kinesin motor domain superfamily	Homologous Superfamily
B, D	IPR001609	Myosin head, motor domain-like	Domain
B, D	IPR002710	Dilute domain	Domain
B, D	IPR000048	IQ motif, EF-hand binding site	Binding Site
B, D	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
B, D	IPR036103	Class V myosin, motor domain	Domain
B, D	IPR037990	Myosin 5b, cargo-binding domain	Domain
B, D	IPR004009	Myosin, N-terminal, SH3-like	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, C	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, D	Pharos: Q9ULV0	microvillus inclusion disease amphetamine abuse liver cancer inborn errors of metabolism intestinal disease pancreatic intraductal papillary-mucinous carcinoma primitive neuroectodermal tumor bowel dysfunction diarrheal disease intellectual disability Intestinal Diseases medulloblastoma non-small cell lung carcinoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia progressive familial intrahepatic cholestasis microvillus inclusion disease amphetamine abuse liver cancer inborn errors of metabolism intestinal disease pancreatic intraductal papillary-mucinous carcinoma primitive neuroectodermal tumor bowel dysfunction diarrheal disease intellectual disability Intestinal Diseases medulloblastoma non-small cell lung carcinoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia progressive familial intrahepatic cholestasis ductal breast carcinoma in situ interstitial cystitis ovarian cancer pituitary cancer schizophrenia liver neoplasm

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.