4DBP | pdb_00004dbp

Myosin VI nucleotide-free (MDINSERT2) D179Y crystal structure

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
B [auth C]	d4dbpc_	All alpha proteins	EF Hand-like	EF-hand	Calmodulin-like	Calmodulin	Fruit fly (Drosophila melanogaster ) [TaxId: 7227 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B [auth C]	SCOP2B Superfamily	EF-hand	8043879	3001983	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)
B [auth C]	EF-hand_1, EF-hand_7	e4dbpC3	A: a/b three-layered sandwiches	X: Fusion glycoprotein F2	H: RIFT-related	T: double psi	F: EF-hand_1, EF-hand_7	ECOD (v294.1)
A	vATP-synt_E	e4dbpA2	A: a/b three-layered sandwiches	X: jelly-roll	H: Acetamidase/Formamidase-like	T: Acetamidase/Formamidase-like	F: vATP-synt_E	ECOD (v294.1)
A	E1_FCCH	e4dbpA4	A: a/b three-layered sandwiches	X: Transmembrane heme-binding four-helical bundle	H: Anticodon-binding domain of Class II aaRS	T: Anticodon-binding domain of Class II aaRS	F: E1_FCCH	ECOD (v294.1)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B [auth C]	PF13499	EF-hand domain pair (EF-hand_7)	EF-hand domain pair		Domain
A	PF00063	Myosin head (motor domain) (Myosin_head)	Myosin head (motor domain)		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B [auth C]	Calmodulin	cation binding ion binding binding calcium ion binding metal ion binding small molecule binding enzyme regulator activity molecular function regulator activity myosin heavy chain binding cytoskeletal protein binding protein binding myosin binding myosin V binding channel regulator activity cation binding ion binding binding calcium ion binding metal ion binding small molecule binding enzyme regulator activity molecular function regulator activity myosin heavy chain binding cytoskeletal protein binding protein binding myosin binding myosin V binding channel regulator activity transporter regulator activity myosin VI binding myosin VI heavy chain binding myosin head/neck binding myosin VI head/neck binding	cellular response to stimulus response to light stimulus regulation of cellular process response to stimulus regulation of response to external stimulus signaling negative regulation of signaling regulation of opsin-mediated signaling pathway negative regulation of biological process regulation of signal transduction detection of abiotic stimulus negative regulation of G protein-coupled receptor signaling pathway negative regulation of cell communication cellular response to environmental stimulus cell communication cellular response to stimulus response to light stimulus regulation of cellular process response to stimulus regulation of response to external stimulus signaling negative regulation of signaling regulation of opsin-mediated signaling pathway negative regulation of biological process regulation of signal transduction detection of abiotic stimulus negative regulation of G protein-coupled receptor signaling pathway negative regulation of cell communication cellular response to environmental stimulus cell communication cellular response to light stimulus negative regulation of cellular process signal transduction regulation of G protein-coupled receptor signaling pathway negative regulation of opsin-mediated signaling pathway detection of light stimulus phototransduction detection of external stimulus regulation of biological process regulation of signaling negative regulation of response to stimulus biological regulation response to external stimulus detection of visible light cellular response to radiation negative regulation of signal transduction detection of stimulus regulation of response to stimulus negative regulation of response to external stimulus regulation of cell communication response to radiation response to abiotic stimulus cellular process G protein-coupled receptor signaling pathway cellular response to abiotic stimulus G protein-coupled opsin signaling pathway phototransduction, visible light multicellular organismal process system process sensory perception of chemical stimulus sensory perception nervous system process sensory perception of smell centriole assembly microtubule organizing center organization organelle assembly microtubule cytoskeleton organization membraneless organelle assembly cellular component organization cellular component biogenesis centrosome duplication organelle organization cellular component assembly centrosome cycle microtubule-based process cell cycle cellular component organization or biogenesis cytoskeleton organization centriole replication cell cycle process autophagic cell death cell death programmed cell death kinetochore organization chromosome organization negative regulation of phospholipase C-activating phototransduction signaling pathway negative regulation of phospholipase C-activating G protein-coupled receptor signaling pathway phospholipase C-activating G protein-coupled receptor signaling pathway phospholipase C-activating opsin-mediated signaling pathway regulation of phospholipase C-activating G protein-coupled receptor signaling pathway response to chemical detection of chemical stimulus detection of chemical stimulus involved in sensory perception of smell detection of stimulus involved in sensory perception detection of chemical stimulus involved in sensory perception response to alcohol response to oxygen-containing compound cellular response to oxygen-containing compound cellular response to chemical stimulus cellular response to alcohol cellular response to ethanol response to ethanol sensory perception of sound sensory perception of mechanical stimulus axonogenesis cellular developmental process cell projection organization plasma membrane bounded cell projection morphogenesis cell development neuron projection development cell morphogenesis neurogenesis multicellular organism development cell projection morphogenesis neuron differentiation neuron projection morphogenesis cell differentiation anatomical structure development system development developmental process plasma membrane bounded cell projection organization axon guidance nervous system development axon development cell morphogenesis involved in neuron differentiation generation of neurons anatomical structure morphogenesis neuron projection guidance neuron development photoreceptor cell axon guidance rhabdomere development sensory organ development photoreceptor cell differentiation visual system development eye morphogenesis compound eye morphogenesis eye photoreceptor cell differentiation animal organ morphogenesis sensory system development photoreceptor cell development eye development eye photoreceptor cell development animal organ development compound eye photoreceptor development compound eye development sensory organ morphogenesis compound eye photoreceptor cell differentiation actin filament-based process actin filament-based movement cellular homeostasis homeostatic process muscle cell cellular homeostasis	midbody cellular anatomical structure cell periphery cell cortex intracellular anatomical structure cytoplasm intracellular organelle centrosome microtubule organizing center cytoskeleton organelle membraneless organelle intracellular membraneless organelle microtubule cytoskeleton midbody cellular anatomical structure cell periphery cell cortex intracellular anatomical structure cytoplasm intracellular organelle centrosome microtubule organizing center cytoskeleton organelle membraneless organelle intracellular membraneless organelle microtubule cytoskeleton centriole cytosol cell projection rhabdomere plasma membrane bounded cell projection mitotic spindle spindle membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen protein-containing complex actin cytoskeleton myosin complex myosin V complex unconventional myosin complex myosin VII complex myosin VI complex mitotic spindle pole spindle pole
A	Myosin-VI	cytoskeletal protein binding actin binding protein-containing complex binding protein binding binding actin filament binding cytoskeletal motor activity adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding cytoskeletal protein binding actin binding protein-containing complex binding protein binding binding actin filament binding cytoskeletal motor activity adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding ADP binding calmodulin binding polypeptide conformation or assembly isomerase activity isomerase activity microfilament motor activity macromolecular conformation isomerase activity catalytic activity ATP-dependent activity	developmental process ear morphogenesis embryonic organ morphogenesis multicellular organismal process ear development sensory organ development animal organ development embryonic morphogenesis embryo development multicellular organism development anatomical structure morphogenesis sensory organ morphogenesis inner ear development inner ear morphogenesis anatomical structure development developmental process ear morphogenesis embryonic organ morphogenesis multicellular organismal process ear development sensory organ development animal organ development embryonic morphogenesis embryo development multicellular organism development anatomical structure morphogenesis sensory organ morphogenesis inner ear development inner ear morphogenesis anatomical structure development animal organ morphogenesis embryonic organ development localization import into cell transport cellular process endocytosis establishment of localization vesicle-mediated transport cellular localization establishment of protein localization intracellular transport protein transport establishment of localization in cell macromolecule localization intracellular protein localization intracellular protein transport regulation of localization regulation of biological process regulation of transport secretion biological regulation regulation of secretion system process sensory perception nervous system process sensory perception of sound sensory perception of mechanical stimulus cellular developmental process epidermis development epithelial cell differentiation hair cell differentiation neurogenesis neuron differentiation cell differentiation system development mechanoreceptor differentiation epithelium development epidermal cell differentiation inner ear auditory receptor cell differentiation nervous system development tissue development inner ear receptor cell differentiation generation of neurons cellular response to stimulus regulation of cellular process response to stimulus signaling signal transduction by p53 class mediator DNA damage response, signal transduction by p53 class mediator intracellular signal transduction cell communication cellular response to stress DNA damage response response to stress signal transduction in response to DNA damage signal transduction cellular component organization organelle organization actin cytoskeleton organization actin filament organization actin filament-based process cellular component organization or biogenesis supramolecular fiber organization cytoskeleton organization actin filament-based movement	cell periphery cell cortex cellular anatomical structure intracellular anatomical structure cytoplasm membrane-bounded organelle nuclear membrane membrane nucleus intracellular membrane-bounded organelle endomembrane system intracellular organelle organelle envelope organelle cell periphery cell cortex cellular anatomical structure intracellular anatomical structure cytoplasm membrane-bounded organelle nuclear membrane membrane nucleus intracellular membrane-bounded organelle endomembrane system intracellular organelle organelle envelope organelle nuclear envelope organelle membrane ruffle cell leading edge plasma membrane leading edge membrane plasma membrane bounded cell projection cell projection ruffle membrane plasma membrane region cell projection membrane intracellular vesicle cytoplasmic vesicle clathrin-coated vesicle coated vesicle vesicle cytoskeleton membraneless organelle intracellular membraneless organelle actin cytoskeleton cytosol membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen protein-containing complex myosin complex Golgi apparatus actin-based cell projection microvillus perinuclear region of cytoplasm polymeric cytoskeletal fiber actin filament supramolecular fiber supramolecular polymer supramolecular complex filamentous actin filopodium

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B [auth C]	IPR002048	EF-hand domain	Domain
B [auth C]	IPR011992	EF-hand domain pair	Homologous Superfamily
B [auth C]	IPR050230	Calmodulin/Myosin light chain/Troponin C-like	Family
B [auth C]	IPR018247	EF-Hand 1, calcium-binding site	Binding Site
A	IPR036961	Kinesin motor domain superfamily	Homologous Superfamily
A	IPR001609	Myosin head, motor domain-like	Domain
A	IPR049016	Myosin VI, lever arm	Domain
A	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
A	IPR004009	Myosin, SH3 domain	Domain
A	IPR036114	Class VI myosin, motor domain	Domain
A	IPR032412	Myosin VI, cargo binding domain	Domain
A	IPR008989	Myosin S1 fragment, N-terminal	Homologous Superfamily

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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.