7PMD

Cryo-EM structure of the actomyosin-V complex in the post-rigor transition state (AppNHp, central 1er)

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations
Protein Modification Annotation

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	P-loop motor domain	8032926	3002036	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Myosin s1 fragment, N-terminal domain	8032925	3000319	SCOP2B (2022-06-29)
B [auth C]	SCOP2B Superfamily	Actin-like ATPases	8040506	3000092	SCOP2B (2022-06-29)
B [auth C]	SCOP2B Superfamily	Actin-like ATPases	8040509	3000092	SCOP2B (2022-06-29)
D [auth B]	SCOP2B Superfamily	EF-hand	8032927	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)
A	Myosin_N_1	e7pmdA1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: Myosin_N_1	ECOD (1.6)
A	IQ_1	e7pmdA3	A: alpha bundles	X: Myosin VI lever arm (From Topology)	H: Myosin VI lever arm (From Topology)	T: Myosin VI lever arm	F: IQ_1	ECOD (1.6)
A	Myosin_head	e7pmdA2	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Myosin_head	ECOD (1.6)
B [auth C]	Actin_1st	e7pmdC2	A: mixed a+b and a/b	X: Ribonuclease H-like	H: Ribonuclease H-like (From Topology)	T: Ribonuclease H-like	F: Actin_1st	ECOD (1.6)
B [auth C]	Actin_2nd	e7pmdC1	A: mixed a+b and a/b	X: Ribonuclease H-like	H: Ribonuclease H-like (From Topology)	T: Ribonuclease H-like	F: Actin_2nd	ECOD (1.6)
D [auth B]	EF-hand_7_8	e7pmdB2	A: alpha arrays	X: EF-hand	H: EF-hand-related	T: EF-hand	F: EF-hand_7_8	ECOD (1.6)
D [auth B]	EF-hand_7_5	e7pmdB1	A: alpha arrays	X: EF-hand	H: EF-hand-related	T: EF-hand	F: EF-hand_7_5	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF00612	IQ calmodulin-binding motif (IQ)	IQ calmodulin-binding motif	-	Motif
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
A	Unconventional myosin-Va	cytoskeletal protein binding actin binding protein-containing complex binding protein binding 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 cytoskeletal protein binding actin binding protein-containing complex binding protein binding 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 minus-end directed microfilament motor activity microfilament motor activity ATP-dependent activity	protein localization localization protein localization to cell periphery cellular localization protein localization to plasma membrane cellular macromolecule localization macromolecule localization cellular process localization within membrane protein localization to membrane transport establishment of localization vesicle-mediated transport cellular response to stimulus protein localization localization protein localization to cell periphery cellular localization protein localization to plasma membrane cellular macromolecule localization macromolecule localization cellular process localization within membrane protein localization to membrane transport establishment of localization vesicle-mediated transport cellular response to stimulus cellular response to nitrogen compound response to stimulus response to endogenous stimulus response to organonitrogen compound 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 cellular response to organonitrogen compound response to hormone response to chemical response to insulin cellular response to insulin stimulus cellular response to hormone stimulus vesicle transport along actin filament vesicle cytoskeletal trafficking vesicle localization establishment of organelle localization establishment of vesicle localization intracellular transport actin filament-based movement organelle localization establishment of localization in cell 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	membrane cellular anatomical entity membrane-bounded organelle organelle vesicle intracellular organelle intracellular anatomical structure cytoskeleton intracellular non-membrane-bounded organelle actin cytoskeleton non-membrane-bounded organelle cytoplasm protein-containing complex myosin complex membrane cellular anatomical entity membrane-bounded organelle organelle vesicle intracellular organelle intracellular anatomical structure cytoskeleton intracellular non-membrane-bounded organelle actin cytoskeleton non-membrane-bounded organelle cytoplasm protein-containing complex myosin complex Golgi membrane Golgi apparatus intracellular membrane-bounded organelle endomembrane system bounding membrane of organelle organelle membrane polymeric cytoskeletal fiber actin filament filamentous actin supramolecular fiber supramolecular polymer supramolecular complex intracellular vesicle insulin-responsive compartment cytoplasmic vesicle secretory granule secretory vesicle
B [auth C]	Actin, alpha skeletal muscle	cytoskeletal protein binding titin binding protein binding binding cation binding ion binding calcium ion binding metal ion binding small molecule binding protein domain specific binding hydrolase activity catalytic activity troponin I binding cytoskeletal motor activator activity cytoskeletal protein binding titin binding protein binding binding cation binding ion binding calcium ion binding metal ion binding small molecule binding protein domain specific binding hydrolase activity catalytic activity troponin I binding cytoskeletal motor activator activity cytoskeletal motor regulator activity molecular function activator activity molecular function regulator activity magnesium ion binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding myosin heavy chain binding myosin binding tropomyosin binding calcium-dependent protein binding identical protein binding actin monomer binding actin binding	developmental process mesenchyme migration multicellular organismal process mesenchyme morphogenesis animal organ development mesenchyme development tissue development tissue morphogenesis anatomical structure morphogenesis tissue migration anatomical structure development animal organ morphogenesis myotube cell development skeletal muscle fiber development developmental process mesenchyme migration multicellular organismal process mesenchyme morphogenesis animal organ development mesenchyme development tissue development tissue morphogenesis anatomical structure morphogenesis tissue migration anatomical structure development animal organ morphogenesis myotube cell development skeletal muscle fiber development cellular developmental process skeletal muscle tissue development cell development muscle cell differentiation myotube differentiation muscle structure development skeletal muscle organ development muscle cell development cell differentiation cellular process muscle tissue development muscle organ development striated muscle cell differentiation regulation of cellular process cellular biosynthetic process positive regulation of biological process positive regulation of cellular metabolic process positive regulation of macromolecule biosynthetic process positive regulation of metabolic process positive regulation of biosynthetic process positive regulation of macromolecule metabolic process positive regulation of cellular process regulation of biosynthetic process regulation of biological process cellular metabolic process biological regulation regulation of cellular metabolic process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulation of cellular biosynthetic process regulation of gene expression biosynthetic process positive regulation of gene expression regulation of macromolecule biosynthetic process metabolic process macromolecule metabolic process regulation of metabolic process positive regulation of cellular biosynthetic process cellular component assembly involved in morphogenesis non-membrane-bounded organelle assembly skeletal myofibril assembly cellular component organization cellular component biogenesis striated muscle cell development cellular anatomical entity morphogenesis cellular component assembly actin filament-based process cellular component organization or biogenesis skeletal muscle thin filament assembly actin cytoskeleton organization actomyosin structure organization organelle assembly actin filament organization organelle organization myofibril assembly anatomical structure formation involved in morphogenesis supramolecular fiber organization cytoskeleton organization protein polymerization actin polymerization or depolymerization actin filament polymerization protein-containing complex organization protein-containing complex assembly actin filament bundle organization actin filament bundle assembly	intracellular anatomical structure skeletal muscle myofibril cellular anatomical entity intracellular organelle organelle intracellular non-membrane-bounded organelle contractile muscle fiber cytoplasm supramolecular fiber myofibril supramolecular polymer supramolecular complex non-membrane-bounded organelle cell projection intracellular anatomical structure skeletal muscle myofibril cellular anatomical entity intracellular organelle organelle intracellular non-membrane-bounded organelle contractile muscle fiber cytoplasm supramolecular fiber myofibril supramolecular polymer supramolecular complex non-membrane-bounded organelle cell projection cell leading edge plasma membrane bounded cell projection lamellipodium cytoskeleton actin filament bundle actin cytoskeleton actomyosin stress fiber contractile actin filament bundle polymeric cytoskeletal fiber actin filament protein-containing complex filamentous actin cell body striated muscle thin filament myofilament sarcomere actin-based cell projection filopodium
C [auth H]	Phalloidin	-	-	-
D [auth B]	Myosin light chain 6B	cation binding ion binding binding calcium ion binding metal ion binding small molecule binding structural molecule activity structural constituent of muscle cytoskeletal motor activity	multicellular organismal process system process muscle contraction muscle system process developmental process muscle structure development skeletal muscle organ development skeletal muscle tissue development anatomical structure development animal organ development muscle tissue development muscle organ development tissue development muscle filament sliding multicellular organismal process system process muscle contraction muscle system process developmental process muscle structure development skeletal muscle organ development skeletal muscle tissue development anatomical structure development animal organ development muscle tissue development muscle organ development tissue development muscle filament sliding actin filament-based process cellular process actin-mediated cell contraction actin filament-based movement actin-myosin filament sliding	protein-containing complex intracellular anatomical structure cellular anatomical entity actin cytoskeleton myosin complex intracellular organelle cytoskeleton organelle intracellular non-membrane-bounded organelle myosin II complex non-membrane-bounded organelle contractile muscle fiber cytoplasm supramolecular fiber protein-containing complex intracellular anatomical structure cellular anatomical entity actin cytoskeleton myosin complex intracellular organelle cytoskeleton organelle intracellular non-membrane-bounded organelle myosin II complex non-membrane-bounded organelle contractile muscle fiber cytoplasm supramolecular fiber muscle myosin complex supramolecular polymer supramolecular complex extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region extracellular space vesicle extracellular membrane-bounded organelle cytosol unconventional myosin complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR036961	Kinesin motor domain superfamily	Homologous Superfamily
A	IPR002710	Dilute domain	Domain
A	IPR000048	IQ motif, EF-hand binding site	Binding Site
A	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
A	IPR036103	Class V myosin, motor domain	Domain
A	IPR037988	Myosin 5a, cargo-binding domain	Domain
A	IPR001609	Myosin head, motor domain	Domain
A	IPR004009	Myosin, N-terminal, SH3-like	Domain
B [auth C]	IPR020902	Actin/actin-like conserved site	Conserved Site
B [auth C]	IPR043129	ATPase, nucleotide binding domain	Homologous Superfamily
B [auth C]	IPR004001	Actin, conserved site	Conserved Site
B [auth C]	IPR004000	Actin family	Family
D [auth B]	IPR050230	Calcium-Regulated Muscle Contraction and Cellular Process	Family
D [auth B]	IPR002048	EF-hand domain	Domain
D [auth B]	IPR011992	EF-hand domain pair	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
D [auth B]	Pharos: P14649	keloid allergic rhinitis asthma ovarian cancer alopecia areata attention deficit hyperactivity disorder, inattentive type lung cancer polycystic ovary syndrome anorexia nervosa Hashimoto thyroiditis myopathy

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
B [auth C]	HIC	Parent Component: HIS RESID: AA0317 PSI-MOD : 1'-methyl-L-histidine MOD:00322
C [auth H]	DTH	RESID: AA0317 , AA0199 PSI-MOD : 1'-methyl-L-histidine MOD:00322 , D-allo-threonine MOD:00863
C [auth H]	EEP	RESID: AA0317 , AA0199
C [auth H]	HYP	Parent Component: PRO RESID: AA0317 , AA0199 , AA0030 PSI-MOD : 1'-methyl-L-histidine MOD:00322 , D-allo-threonine MOD:00863 , 4-hydroxy-L-proline MOD:00039

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 R01GM133198.