5SZJ

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

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	d5szja_	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	SCOP2B Superfamily	Ras-like P-loop GTPases	8060214	3002022	SCOP2B (2022-06-29)
B	SCOP2 Family	Mical/EHBP Rab binding (bMERB) domain-like	8047250	4005529	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	Mical/EHBP Rab binding (bMERB) domain-like	8092903	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	e5szjA1	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	e5szjB1	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)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	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	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	MICAL C-terminal-like protein	oxidoreductase activity catalytic activity FAD binding flavin adenine dinucleotide binding 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 catalytic activity FAD binding flavin adenine dinucleotide binding 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 NAD(P)H oxidase H2O2-forming activity oxidoreductase activity, acting on NAD(P)H oxidoreductase activity, acting on NAD(P)H, oxygen as acceptor cytoskeletal protein binding actin binding protein binding kinase binding enzyme binding protein kinase binding mitogen-activated protein kinase binding cation binding metal ion binding	developmental process heart development multicellular organism development multicellular organismal process anatomical structure development animal organ development circulatory system development system development sulfur compound metabolic process metabolic process cellular process sulfur oxidation cellular component disassembly actin polymerization or depolymerization developmental process heart development multicellular organism development multicellular organismal process anatomical structure development animal organ development circulatory system development system development sulfur compound metabolic process metabolic process cellular process sulfur oxidation 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 cellular process positive regulation of DNA-templated transcription positive regulation of biological process RNA metabolic process positive regulation of macromolecule biosynthetic process regulation of primary metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process positive regulation of metabolic process DNA-templated transcription regulation of RNA metabolic process transcription by RNA polymerase II positive regulation of biosynthetic process positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process positive regulation of cellular process regulation of RNA biosynthetic process regulation of biosynthetic process regulation of transcription by RNA polymerase II regulation of biological process positive regulation of nucleobase-containing compound metabolic process biological regulation primary metabolic process regulation of macromolecule metabolic process positive regulation of transcription by RNA polymerase II nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process positive regulation of RNA metabolic process regulation of gene expression biosynthetic process positive regulation of RNA biosynthetic process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of DNA-templated transcription regulation of metabolic process heart morphogenesis pattern specification process embryo development embryonic heart tube development tube morphogenesis embryonic heart tube morphogenesis heart looping determination of bilateral symmetry animal organ morphogenesis epithelial tube morphogenesis embryonic organ development determination of left/right symmetry specification of symmetry embryonic organ morphogenesis epithelium development tube development embryonic morphogenesis morphogenesis of an epithelium determination of heart left/right asymmetry tissue development regionalization anatomical structure morphogenesis tissue morphogenesis left/right pattern formation	cellular anatomical structure intracellular anatomical structure cytoplasm polymeric cytoskeletal fiber actin filament intracellular membraneless organelle actin cytoskeleton intracellular organelle cytoskeleton organelle membraneless organelle supramolecular fiber supramolecular polymer supramolecular complex cellular anatomical structure intracellular anatomical structure cytoplasm polymeric cytoskeletal fiber actin filament intracellular membraneless organelle actin cytoskeleton intracellular organelle cytoskeleton organelle membraneless organelle supramolecular fiber supramolecular polymer supramolecular complex membrane-bounded organelle nucleus intracellular membrane-bounded organelle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
A	IPR050305	Small GTPase superfamily, Rab	Family
A	IPR005225	Small GTP-binding domain	Domain
A	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
B	IPR016103	ProQ/FinO domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	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: O94851	medulloblastoma osteosarcoma pancreatic intraductal papillary-mucinous neoplasm primitive neuroectodermal tumor adrenal cortex carcinoma breast cancer dermatomyositis exocrine pancreatic carcinoma invasive ductal breast carcinoma lung carcinoma malignant mesothelioma nasopharyngeal carcinoma ovarian cancer Pick disease subependymal giant cell astrocytoma medulloblastoma osteosarcoma pancreatic intraductal papillary-mucinous neoplasm primitive neuroectodermal tumor adrenal cortex carcinoma breast cancer dermatomyositis exocrine pancreatic carcinoma invasive ductal breast carcinoma lung carcinoma malignant mesothelioma nasopharyngeal carcinoma ovarian cancer Pick disease subependymal giant cell astrocytoma astrocytic tumor breast carcinoma Down syndrome gastric carcinoma large cell medulloblastoma malignant ependymoma malignant pancreatic neoplasm oligodendroglioma pancreatic ductal adenocarcinoma pilocytic astrocytoma tuberculosis atypical teratoid rhabdoid tumor chronic kidney disease ductal breast carcinoma in situ glioblastoma lung cancer malignant glioma

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.