5LPN

Structure of human Rab10 in complex with the bMERB domain of Mical-1

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	d5lpna_	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	automated matches	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d5lpnc_	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	automated matches	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	SCOP2 Family	Ras-like monodomain GTPases	8060213	4004043	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Ras-like P-loop GTPases	8060214	3002022	SCOP2 (2022-06-29)
C	SCOP2B Superfamily	Ras-like P-loop GTPases	8060214	3002022	SCOP2B (2022-06-29)
B	SCOP2 Family	Mical/EHBP Rab binding (bMERB) domain-like	8047252	4005529	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	Mical/EHBP Rab binding (bMERB) domain-like	8092905	3002641	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	e5lpnA1	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	e5lpnC1	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	DUF3585	e5lpnB1	A: alpha bundles	X: Long alpha-hairpin	H: bMERB domain (bivalent Mical/EHBP Rab binding) (From Topology)	T: bMERB domain (bivalent Mical/EHBP Rab binding)	F: DUF3585	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	PF12130	Bivalent Mical/EHBP Rab binding domain (bMERB_dom)	Bivalent Mical/EHBP Rab binding domain	A variety of different effector proteins interact specifically with GTP-bound Rab proteins and mediate their versatile roles in membrane trafficking, including budding of vesicles from a donor membrane, directed transport through the cell and finally ...	A variety of different effector proteins interact specifically with GTP-bound Rab proteins and mediate their versatile roles in membrane trafficking, including budding of vesicles from a donor membrane, directed transport through the cell and finally tethering and fusion with a target membrane. The 'bivalent Mical/EHBP Rab binding' (bMERB) domain is a Rab effector domain that is present in proteins of the Mical and EHBP families, both known to act in endosomal trafficking. The bMERB domain displays a preference for Rab8 family proteins (Rab8, 10, 13 and 15) and at least some of the bMERB domains contain two separate binding sites for Rab-proteins, allowing Micals and EHBPs to bind two Rabs simultaneously. The strong similarity between the two binding sites within one bMRB domain strongly suggests an evolutionarily development via duplication of a common ancestor supersecondary structure element. The bMERB domain has a completely alpha-helical fold consisting of a central helix and N- and C-terminal helices folding back on this central helix [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, C	Ras-related protein Rab-10	cell adhesion molecule binding cadherin binding involved in cell-cell adhesion cadherin binding protein binding binding cell adhesion mediator activity cell-cell adhesion mediator activity guanyl nucleotide binding GTP binding nucleotide binding guanyl ribonucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding cell adhesion molecule binding cadherin binding involved in cell-cell adhesion cadherin binding protein binding binding cell adhesion mediator activity cell-cell adhesion mediator 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 GDP binding cytoskeletal protein binding myosin V binding myosin binding pyrophosphatase activity GTPase activity G protein activity ribonucleoside triphosphate phosphatase activity molecular function regulator activity hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides hydrolase activity hydrolase activity, acting on acid anhydrides catalytic 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 neuroblast proliferation multicellular organismal process cellular developmental process establishment or maintenance of cell polarity establishment of neuroblast polarity neurogenesis multicellular organism development asymmetric neuroblast division cell differentiation anatomical structure development system development developmental process cell population proliferation neuroblast division nervous system development asymmetric cell division establishment or maintenance of neuroblast polarity generation of neurons establishment of cell polarity cell division neural precursor cell proliferation cell fate commitment axonogenesis cell projection organization plasma membrane bounded cell projection morphogenesis cell development neuron projection development cell morphogenesis cellular component organization cell projection morphogenesis neuron differentiation neuron projection morphogenesis cellular component organization or biogenesis plasma membrane bounded cell projection organization axon development cell morphogenesis involved in neuron differentiation anatomical structure morphogenesis neuron development establishment of localization in cell intracellular transport endosomal transport establishment of protein localization to endoplasmic reticulum membrane establishment of protein localization to organelle protein localization to organelle establishment of protein localization to endoplasmic reticulum protein localization to endoplasmic reticulum regulated exocytosis secretion by cell exocytosis secretion export from cell establishment of protein localization to extracellular region protein secretion protein localization to extracellular region protein localization to basolateral plasma membrane polarized epithelial cell differentiation epithelium development morphogenesis of an epithelium tissue development epithelial cell differentiation tissue morphogenesis morphogenesis of a polarized epithelium organelle organization endoplasmic reticulum tubular network organization endoplasmic reticulum organization endomembrane system organization antigen processing and presentation immune system process cellular response to nitrogen compound cellular response to stimulus response to stimulus response to endogenous stimulus response to peptide hormone response to oxygen-containing compound cellular response to peptide hormone stimulus response to nitrogen compound cellular response to oxygen-containing compound cellular response to endogenous stimulus cellular response to chemical stimulus response to hormone response to chemical response to insulin cellular response to insulin stimulus cellular response to hormone stimulus	cellular anatomical structure membrane extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle extracellular space vesicle extracellular membrane-bounded organelle intracellular anatomical structure cytoplasm cytosol cellular anatomical structure membrane extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle extracellular space vesicle extracellular membrane-bounded organelle intracellular anatomical structure cytoplasm cytosol cell-cell junction adherens junction anchoring junction cell junction intracellular vesicle phagocytic vesicle intracellular membrane-bounded organelle intracellular organelle phagocytic vesicle membrane 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 cytoskeleton membraneless organelle intracellular membraneless organelle Golgi membrane endosome recycling endosome perinuclear region of cytoplasm endosome membrane insulin-responsive compartment secretory granule secretory vesicle cell projection cilium plasma membrane bounded cell projection focal adhesion cell-substrate junction transport vesicle exocytic vesicle cell periphery plasma membrane lytic vacuole vacuole lysosome endoplasmic reticulum subcompartment nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum endoplasmic reticulum membrane recycling endosome membrane secretory granule membrane endoplasmic reticulum tubular network
B	Protein-methionine sulfoxide oxidase MICAL1	small GTPase binding protein binding binding enzyme binding GTPase binding cytoskeletal protein binding actin binding protein-containing complex binding actin filament binding NAD(P)H oxidase H2O2-forming activity oxidoreductase activity NADPH oxidase H202-forming activity oxidoreductase activity, acting on NAD(P)H catalytic activity small GTPase binding protein binding binding enzyme binding GTPase binding cytoskeletal protein binding actin binding protein-containing complex binding actin filament binding NAD(P)H oxidase H2O2-forming activity oxidoreductase activity NADPH oxidase H202-forming activity oxidoreductase activity, acting on NAD(P)H catalytic activity oxidoreductase activity, acting on NAD(P)H, oxygen as acceptor FAD binding flavin adenine dinucleotide binding nucleoside phosphate binding ion binding organic cyclic compound binding anion binding nucleotide binding heterocyclic compound binding small molecule binding monooxygenase activity F-actin monooxygenase activity oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen SH3 domain binding protein domain specific binding kinase binding protein kinase binding cation binding metal ion binding	sulfur compound metabolic process metabolic process cellular process sulfur oxidation regulation of cellular process regulation of protein modification process regulation of protein phosphorylation negative regulation of biological process negative regulation of phosphate metabolic process regulation of primary metabolic process regulation of phosphate metabolic process phosphate-containing compound metabolic process negative regulation of protein modification process negative regulation of cellular process sulfur compound metabolic process metabolic process cellular process sulfur oxidation regulation of cellular process regulation of protein modification process regulation of protein phosphorylation negative regulation of biological process negative regulation of phosphate metabolic process regulation of primary metabolic process regulation of phosphate metabolic process phosphate-containing compound metabolic process negative regulation of protein modification process negative regulation of cellular process protein metabolic process protein modification process phosphorus metabolic process negative regulation of protein metabolic process negative regulation of macromolecule metabolic process regulation of biological process protein phosphorylation phosphorylation regulation of protein metabolic process negative regulation of metabolic process biological regulation primary metabolic process regulation of macromolecule metabolic process negative regulation of protein phosphorylation macromolecule modification negative regulation of phosphorus metabolic process regulation of phosphorylation regulation of phosphorus metabolic process macromolecule metabolic process negative regulation of phosphorylation regulation of metabolic process cellular component disassembly actin polymerization or depolymerization actin cytoskeleton organization protein-containing complex organization actin filament organization protein-containing complex disassembly actin filament depolymerization cellular component organization organelle organization actin filament-based process cellular component organization or biogenesis supramolecular fiber organization protein depolymerization cytoskeleton organization regulation of localization regulated exocytosis transport secretion regulation of transport export from cell regulation of vesicle-mediated transport establishment of localization vesicle-mediated transport regulation of secretion regulation of regulated secretory pathway localization secretion by cell regulation of secretion by cell exocytosis regulation of exocytosis cellular response to stimulus response to stimulus signaling signal transduction cell communication cellular component biogenesis cellular component assembly actin filament bundle organization actin filament bundle assembly	midbody cellular anatomical structure polymeric cytoskeletal fiber intracellular anatomical structure intracellular membraneless organelle intermediate filament cytoskeleton intracellular organelle cytoskeleton organelle membraneless organelle intermediate filament supramolecular fiber supramolecular polymer supramolecular complex midbody cellular anatomical structure polymeric cytoskeletal fiber intracellular anatomical structure intracellular membraneless organelle intermediate filament cytoskeleton intracellular organelle cytoskeleton organelle membraneless organelle intermediate filament supramolecular fiber supramolecular polymer supramolecular complex actin cytoskeleton cytoplasm cytosol cell periphery plasma membrane membrane axon synapse hippocampal mossy fiber expansion neuron projection axon terminus plasma membrane bounded cell projection hippocampal mossy fiber presynapse cell projection distal axon terminal bouton cell junction neuron projection terminus intercellular bridge endosome membrane membrane-bounded organelle endosome intracellular vesicle intracellular membrane-bounded organelle endomembrane system cytoplasmic vesicle membrane bounding membrane of organelle vesicle membrane cytoplasmic vesicle vesicle organelle membrane actin filament

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, C	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
A, C	IPR050305	Small GTPase superfamily, Rab	Family
A, C	IPR005225	Small GTP-binding domain	Domain
A, C	IPR001806	Small GTPase	Family
B	IPR036188	FAD/NAD(P)-binding domain superfamily	Homologous Superfamily
B	IPR050540	F-actin Monooxygenase Mical	Family
B	IPR001715	Calponin homology domain	Domain
B	IPR002938	FAD-binding domain	Domain
B	IPR022735	bMERB domain	Domain
B	IPR001781	Zinc finger, LIM-type	Domain
B	IPR036872	CH domain superfamily	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, C	Pharos: P61026	atrial fibrillation invasive ductal breast carcinoma neurodegenerative disease ovarian cancer tuberculosis breast cancer limb-girdle muscular dystrophy non-small cell lung carcinoma pancreatic ductal adenocarcinoma hepatocellular carcinoma malignant pancreatic neoplasm osteosarcoma psoriasis
B	Pharos: Q8TDZ2	Autosomal dominant epilepsy with auditory features Malignant neoplasm of breast oligodendroglioma pancreatic ductal adenocarcinoma Pick disease gastric carcinoma medulloblastoma osteosarcoma pancreatic intraductal papillary-mucinous carcinoma spina bifida malignant mesothelioma non-small cell lung carcinoma ovarian cancer 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.