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- PDB-6z47: Smooth muscle myosin shutdown state heads region -

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Basic information

Entry
Database: PDB / ID: 6z47
TitleSmooth muscle myosin shutdown state heads region
Components
  • (Myosin light chain ...) x 2
  • Myosin heavy chain 11
KeywordsCONTRACTILE PROTEIN / myosin / motor / inhibited state / shutdown state / smooth muscle
Function / homology
Function and homology information


myofibril assembly / myosin filament / actomyosin structure organization / myosin II complex / structural constituent of muscle / microfilament motor activity / myofibril / stress fiber / platelet aggregation / actin filament binding ...myofibril assembly / myosin filament / actomyosin structure organization / myosin II complex / structural constituent of muscle / microfilament motor activity / myofibril / stress fiber / platelet aggregation / actin filament binding / calcium ion binding / ATP binding / cytosol
Similarity search - Function
: / EF-hand domain / DNA repair protein XRCC4-like, C-terminal / Myosin tail / Myosin tail / Myosin N-terminal SH3-like domain / Myosin S1 fragment, N-terminal / EF-hand domain pair / : / Myosin, N-terminal, SH3-like ...: / EF-hand domain / DNA repair protein XRCC4-like, C-terminal / Myosin tail / Myosin tail / Myosin N-terminal SH3-like domain / Myosin S1 fragment, N-terminal / EF-hand domain pair / : / Myosin, N-terminal, SH3-like / Myosin N-terminal SH3-like domain profile. / Short calmodulin-binding motif containing conserved Ile and Gln residues. / IQ motif, EF-hand binding site / Myosin head, motor domain / Myosin head (motor domain) / Myosin motor domain profile. / Myosin. Large ATPases. / IQ motif profile. / Kinesin motor domain superfamily / EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / PHOSPHATE ION / Myosin-11 / EF-hand domain-containing protein / Myosin light chain smooth muscle isoform
Similarity search - Component
Biological speciesMeleagris gallopavo (turkey)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 6.3 Å
AuthorsScarff, C.A. / Carrington, G. / Casas Mao, D. / Chalovich, J.M. / Knight, P.J. / Ranson, N.A. / Peckham, M.
Funding support United Kingdom, 3items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MR/R009406/1 United Kingdom
Medical Research Council (MRC, United Kingdom)MR/S023593/1 United Kingdom
Wellcome Trust108466/Z/15/Z United Kingdom
CitationJournal: Nature / Year: 2020
Title: Structure of the shutdown state of myosin-2.
Authors: Charlotte A Scarff / Glenn Carrington / David Casas-Mao / Joseph M Chalovich / Peter J Knight / Neil A Ranson / Michelle Peckham /
Abstract: Myosin-2 is essential for processes as diverse as cell division and muscle contraction. Dephosphorylation of its regulatory light chain promotes an inactive, 'shutdown' state with the filament- ...Myosin-2 is essential for processes as diverse as cell division and muscle contraction. Dephosphorylation of its regulatory light chain promotes an inactive, 'shutdown' state with the filament-forming tail folded onto the two heads, which prevents filament formation and inactivates the motors. The mechanism by which this happens is unclear. Here we report a cryo-electron microscopy structure of shutdown smooth muscle myosin with a resolution of 6 Å in the head region. A pseudo-atomic model, obtained by flexible fitting of crystal structures into the density and molecular dynamics simulations, describes interaction interfaces at the atomic level. The N-terminal extension of one regulatory light chain interacts with the tail, and the other with the partner head, revealing how the regulatory light chains stabilize the shutdown state in different ways and how their phosphorylation would allow myosin activation. Additional interactions between the three segments of the coiled coil, the motor domains and the light chains stabilize the shutdown molecule. The structure of the lever in each head is competent to generate force upon activation. This shutdown structure is relevant to all isoforms of myosin-2 and provides a framework for understanding their disease-causing mutations.
History
DepositionMay 22, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 9, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 16, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title ..._citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Dec 30, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3May 22, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

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Assembly

Deposited unit
A: Myosin heavy chain 11
B: Myosin heavy chain 11
C: Myosin light chain smooth muscle isoform
D: Myosin light chain smooth muscle isoform
E: Myosin light chain 9
F: Myosin light chain 9
G: Myosin heavy chain 11
H: Myosin heavy chain 11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)991,45716
Polymers990,3168
Non-polymers1,1428
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Myosin light chain ... , 2 types, 4 molecules CDEF

#2: Protein Myosin light chain smooth muscle isoform


Mass: 16989.145 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Meleagris gallopavo (turkey) / References: UniProt: Q6W5H0
#3: Protein Myosin light chain 9


Mass: 19872.244 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Meleagris gallopavo (turkey) / References: UniProt: G3URE9

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Antibody , 1 types, 4 molecules ABGH

#1: Antibody
Myosin heavy chain 11


Mass: 229148.250 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Meleagris gallopavo (turkey) / Tissue: Gizzard / References: UniProt: G1N5L2

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Non-polymers , 3 types, 8 molecules

#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#6: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4

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Details

Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Smooth muscle myosin in the shutdown state / Type: COMPLEX / Entity ID: #1-#3 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Meleagris gallopavo (turkey)
Buffer solutionpH: 7.2
Buffer component
IDConc.FormulaBuffer-ID
1150 mMKCl1
210 mMMOPS1
30.1 mMEGTA1
42 mMMgCl21
51 mMATP1
SpecimenConc.: 0.45 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: Smooth muscle myosin from turkey gizzard, stored under liquid nitrogen, was thawed quickly. MgATP was added before dilution into the final buffer conditions stated below
Specimen supportDetails: GloCube / Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 281 K / Details: Blot force 6, blot time 3 seconds

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Specimen holderSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 60 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 QUANTUM (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 6.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 96351 / Symmetry type: POINT

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