7PME | pdb_00007pme

Cryo-EM structure of the actomyosin-V complex in the post-rigor transition state (AppNHp, central 3er/2er)

External Resource: Annotation

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
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)
E [auth D]	SCOP2B Superfamily	P-loop motor domain	8032926	3002036	SCOP2B (2022-06-29)
E [auth D]	SCOP2B Superfamily	Myosin s1 fragment, N-terminal domain	8032925	3000319	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	EF-hand	8032927	3001983	SCOP2B (2022-06-29)
F [auth E]	SCOP2B Superfamily	EF-hand	8032927	3001983	SCOP2B (2022-06-29)
G [auth F]	SCOP2B Superfamily	Actin-like ATPases	8040509	3000092	SCOP2B (2022-06-29)
G [auth F]	SCOP2B Superfamily	Actin-like ATPases	8040506	3000092	SCOP2B (2022-06-29)
I [auth G]	SCOP2B Superfamily	Actin-like ATPases	8040509	3000092	SCOP2B (2022-06-29)
I [auth G]	SCOP2B Superfamily	Actin-like ATPases	8040506	3000092	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Actin-like ATPases	8040509	3000092	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Actin-like ATPases	8040506	3000092	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	e7pmeA2	A: beta barrels	X: SH3	H: SH3	T: SH3	F: Myosin_N_1	ECOD (1.6)
A	IQ_1	e7pmeA3	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	e7pmeA1	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)
E [auth D]	Myosin_N_1	e7pmeD2	A: beta barrels	X: SH3	H: SH3	T: SH3	F: Myosin_N_1	ECOD (1.6)
E [auth D]	IQ_1	e7pmeD3	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)
E [auth D]	Myosin_head	e7pmeD1	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	EF-hand_7_8	e7pmeB2	A: alpha arrays	X: EF-hand	H: EF-hand-related	T: EF-hand	F: EF-hand_7_8	ECOD (1.6)
B	EF-hand_7_5	e7pmeB1	A: alpha arrays	X: EF-hand	H: EF-hand-related	T: EF-hand	F: EF-hand_7_5	ECOD (1.6)
F [auth E]	EF-hand_7_8	e7pmeE2	A: alpha arrays	X: EF-hand	H: EF-hand-related	T: EF-hand	F: EF-hand_7_8	ECOD (1.6)
F [auth E]	EF-hand_7_5	e7pmeE1	A: alpha arrays	X: EF-hand	H: EF-hand-related	T: EF-hand	F: EF-hand_7_5	ECOD (1.6)
G [auth F]	Actin_1st	e7pmeF2	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)
G [auth F]	Actin_2nd	e7pmeF1	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)
I [auth G]	Actin_1st	e7pmeG2	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)
I [auth G]	Actin_2nd	e7pmeG1	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)
C	Actin_1st	e7pmeC2	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)
C	Actin_2nd	e7pmeC1	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)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	1.20.58.530	Mainly Alpha	Up-down Bundle	Methane Monooxygenase Hydroxylase	Chain G, domain 1	CATH (utative)
E [auth D]	1.20.58.530	Mainly Alpha	Up-down Bundle	Methane Monooxygenase Hydroxylase	Chain G, domain 1	CATH (utative)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, E [auth D]	PF00612	IQ calmodulin-binding motif (IQ)	IQ calmodulin-binding motif	-	Motif
A, E [auth D]	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, E [auth D]	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 anion 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 anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding calmodulin binding pyrophosphatase activity ATP hydrolysis 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 ATP-dependent activity polypeptide conformation or assembly isomerase activity isomerase activity cytoskeletal motor activity minus-end directed microfilament motor activity microfilament motor activity macromolecular conformation isomerase activity	localization protein localization to cell periphery cellular localization protein localization to plasma membrane macromolecule localization cellular process intracellular protein localization localization within membrane protein localization to membrane transport establishment of localization vesicle-mediated transport cellular response to stimulus cellular response to nitrogen compound localization protein localization to cell periphery cellular localization protein localization to plasma membrane macromolecule localization cellular process intracellular protein localization 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 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 component organization organelle organization actin cytoskeleton organization actin filament organization actin filament-based process cellular component organization or biogenesis supramolecular fiber organization cytoskeleton organization	cellular anatomical structure membrane intracellular organelle intracellular anatomical structure cytoskeleton organelle membraneless organelle intracellular membraneless organelle actin cytoskeleton cytoplasm protein-containing complex myosin complex membrane-bounded organelle Golgi membrane cellular anatomical structure membrane intracellular organelle intracellular anatomical structure cytoskeleton organelle membraneless organelle intracellular membraneless organelle actin cytoskeleton cytoplasm protein-containing complex myosin complex membrane-bounded organelle 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 vesicle
B, F [auth E]	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 striated muscle tissue development 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 striated muscle 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 intracellular membraneless organelle actin cytoskeleton myosin complex intracellular organelle cellular anatomical structure cytoskeleton organelle membraneless organelle myosin II complex contractile muscle fiber cytoplasm supramolecular fiber protein-containing complex intracellular anatomical structure intracellular membraneless organelle actin cytoskeleton myosin complex intracellular organelle cellular anatomical structure cytoskeleton organelle membraneless organelle myosin II complex 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
C, G [auth F], I [auth G]	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 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 striated muscle tissue development muscle structure development skeletal muscle organ development striated muscle cell development muscle cell development cell differentiation cellular process muscle tissue development muscle organ development striated muscle cell differentiation regulation of biosynthetic process regulation of biological process regulation of cellular process biological regulation positive regulation of biological process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process positive regulation of macromolecule biosynthetic process regulation of gene expression positive regulation of metabolic process biosynthetic process positive regulation of gene expression positive regulation of biosynthetic process regulation of macromolecule biosynthetic process metabolic process positive regulation of macromolecule metabolic process macromolecule metabolic process regulation of metabolic process positive regulation of cellular process cellular component assembly involved in morphogenesis skeletal myofibril assembly membraneless organelle assembly cellular component organization cellular component biogenesis 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 intracellular membraneless organelle intracellular organelle cellular anatomical structure organelle membraneless organelle contractile muscle fiber cytoplasm supramolecular fiber myofibril supramolecular polymer supramolecular complex cell projection intracellular anatomical structure skeletal muscle myofibril intracellular membraneless organelle intracellular organelle cellular anatomical structure organelle membraneless organelle contractile muscle fiber cytoplasm supramolecular fiber myofibril supramolecular polymer supramolecular complex 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
D [auth H], H [auth I], J	Phalloidin	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

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

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
B, F [auth E]	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
C, G [auth F], I [auth G]	HIC	Parent Component: HIS RESID: AA0317 PSI-MOD : 1'-methyl-L-histidine MOD:00322
D [auth H], H [auth I], J	DTH	RESID: AA0317 , AA0199 PSI-MOD : 1'-methyl-L-histidine MOD:00322 , D-allo-threonine MOD:00863
D [auth H], H [auth I], J	EEP	RESID: AA0317 , AA0199
D [auth H], H [auth I], J	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 R01GM157729.