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- PDB-9syu: shutdown state non-muscle myosin 2A heads region -

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Basic information

Entry
Database: PDB / ID: 9syu
Titleshutdown state non-muscle myosin 2A heads region
Components
  • (Isoform 1 of ...) x 2
  • Myosin regulatory light polypeptide 9
KeywordsMOTOR PROTEIN / Myosin / coiled coil
Function / homology
Function and homology information


Ephrin signaling / Smooth Muscle Contraction / negative regulation of actin filament severing / uropod organization / regulation of plasma membrane repair / establishment of meiotic spindle localization / cytokinetic process / myosin II filament / cortical granule exocytosis / establishment of T cell polarity ...Ephrin signaling / Smooth Muscle Contraction / negative regulation of actin filament severing / uropod organization / regulation of plasma membrane repair / establishment of meiotic spindle localization / cytokinetic process / myosin II filament / cortical granule exocytosis / establishment of T cell polarity / myofibril assembly / cortical granule / blood vessel endothelial cell migration / actomyosin contractile ring / positive regulation of protein processing in phagocytic vesicle / uropod / regulated exocytosis / myosin II binding / actin filament-based movement / muscle myosin complex / meiotic spindle organization / lysosome localization / plasma membrane repair / actomyosin / myosin filament / myoblast fusion / RHO GTPases activate CIT / RHO GTPases Activate ROCKs / actomyosin structure organization / Sema4D induced cell migration and growth-cone collapse / myosin II complex / Sensory processing of sound by outer hair cells of the cochlea / structural constituent of muscle / platelet formation / CD163 mediating an anti-inflammatory response / Sensory processing of sound by inner hair cells of the cochlea / leukocyte migration / phagocytosis, engulfment / EPHA-mediated growth cone collapse / myosin heavy chain binding / microfilament motor activity / endodermal cell differentiation / cell leading edge / RHO GTPases activate PAKs / cleavage furrow / brush border / membrane protein ectodomain proteolysis / cytoskeletal motor activity / monocyte differentiation / immunological synapse / RHO GTPases activate PKNs / stress fiber / protein-membrane adaptor activity / ruffle / integrin-mediated signaling pathway / Translocation of SLC2A4 (GLUT4) to the plasma membrane / FCGR3A-mediated phagocytosis / adherens junction / neuromuscular junction / ADP binding / Regulation of actin dynamics for phagocytic cup formation / platelet aggregation / spindle / cytoplasmic side of plasma membrane / integrin binding / actin filament binding / Signaling by ALK fusions and activated point mutants / protein transport / regulation of cell shape / actin cytoskeleton / actin binding / virus receptor activity / actin cytoskeleton organization / cell cortex / angiogenesis / in utero embryonic development / calmodulin binding / nuclear body / cadherin binding / protein domain specific binding / focal adhesion / calcium ion binding / symbiont entry into host cell / magnesium ion binding / cell surface / protein homodimerization activity / protein-containing complex / RNA binding / extracellular exosome / ATP binding / identical protein binding / nucleus / membrane / plasma membrane / cytosol / cytoplasm
Similarity search - Function
DJBP, EF-hand domain / EF-hand domain / : / RGS domain superfamily / Myosin tail / Myosin tail / Myosin N-terminal SH3-like domain / Myosin S1 fragment, N-terminal / Myosin, N-terminal, SH3-like / Myosin N-terminal SH3-like domain profile. ...DJBP, EF-hand domain / EF-hand domain / : / RGS domain superfamily / Myosin tail / Myosin tail / Myosin N-terminal SH3-like domain / Myosin S1 fragment, N-terminal / 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 light polypeptide 6 / Myosin-9 / Myosin regulatory light polypeptide 9
Similarity search - Component
Biological speciesHomo sapiens (human)
Gallus gallus (chicken)
Bos taurus (domestic cattle)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.98 Å
AuthorsPeckham, M. / Carrington, G.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome TrustRGIMCB124415 United Kingdom
CitationJournal: To Be Published
Title: Cryo-EM structure of shutdown non-muscle myosin 2A
Authors: Casas-Mao, D. / Carrington, G. / Peckham, M.
History
DepositionOct 14, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 22, 2025Provider: repository / Type: Initial release
Revision 1.0Oct 22, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Oct 22, 2025Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Oct 22, 2025Data content type: Additional map / Part number: 2 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Oct 22, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Oct 22, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Oct 22, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Oct 22, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Oct 22, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Isoform 1 of Myosin-9
B: Isoform 1 of Myosin-9
C: Isoform 1 of Myosin light polypeptide 6
D: Isoform 1 of Myosin light polypeptide 6
E: Myosin regulatory light polypeptide 9
F: Myosin regulatory light polypeptide 9
G: Isoform 1 of Myosin-9
H: Isoform 1 of Myosin-9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)982,48616
Polymers981,3448
Non-polymers1,1428
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Isoform 1 of ... , 2 types, 6 molecules ABGHCD

#1: Protein
Isoform 1 of Myosin-9 / Cellular myosin heavy chain / type A / Myosin heavy chain 9 / Myosin heavy chain / non-muscle IIa / ...Cellular myosin heavy chain / type A / Myosin heavy chain 9 / Myosin heavy chain / non-muscle IIa / Non-muscle myosin heavy chain A / NMMHC-A / Non-muscle myosin heavy chain IIa / NMMHC II-a / NMMHC-IIA


Mass: 226888.781 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MYH9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P35579
#2: Protein Isoform 1 of Myosin light polypeptide 6 / G2 catalytic / LC17-GI / LC17-NM / Myosin light chain alkali smooth-muscle/non-muscle isoforms


Mass: 17004.221 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: MYL6 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P02607

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Protein , 1 types, 2 molecules EF

#3: Protein Myosin regulatory light polypeptide 9 / Myosin regulatory light chain 2 / smooth muscle isoform / Myosin regulatory light chain 9


Mass: 19890.211 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / Gene: MYL9, MYRL2 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q5E9E2

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Non-polymers , 3 types, 8 molecules

#4: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


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


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY
Has protein modificationN

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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: NM2A complex with essential and regulatory light chains in the shutdown state
Type: COMPLEX / Entity ID: #1-#3 / Source: RECOMBINANT
Molecular weightValue: 0.527 MDa / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 7.2
Details: 140 mM KCl, 10 mM MOPS pH 7.2, 0.1 mM EGTA, 2 mM MgCl2, 1 mM ATP. 1 mM Bissulfosuccinimidyl suberate
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid type: UltrAuFoil
VitrificationCryogen name: ETHANE / Humidity: 90 %

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 96000 X / Nominal defocus max: 3000 nm / Nominal defocus min: 900 nm / Cs: 2.7 mm
Specimen holderSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 3.42 sec. / Electron dose: 36.94 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of grids imaged: 2 / Num. of real images: 27549

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Processing

EM software
IDNameVersionCategory
1cryoSPARCv4.7.0particle selection
2EPU3.3image acquisition
4cryoSPARCCTF correction
10cryoSPARCinitial Euler assignment
11cryoSPARCfinal Euler assignment
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.98 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 186265 / Num. of class averages: 1 / Symmetry type: POINT

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