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- PDB-9z4q: Cryo-EM structure of human nonmuscle myosin-2B, Class 3 -

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Basic information

Entry
Database: PDB / ID: 9z4q
TitleCryo-EM structure of human nonmuscle myosin-2B, Class 3
Components
  • Myosin light polypeptide 6
  • Myosin regulatory light chain 12B
  • Myosin-10
KeywordsMOTOR PROTEIN / myosin / ATPase
Function / homology
Function and homology information


myosin II filament / postsynaptic actin cytoskeleton organization / unconventional myosin complex / actin filament-based movement / actomyosin / myosin filament / RHO GTPases Activate ROCKs / postsynaptic actin cytoskeleton / actomyosin structure organization / RHO GTPases activate CIT ...myosin II filament / postsynaptic actin cytoskeleton organization / unconventional myosin complex / actin filament-based movement / actomyosin / myosin filament / RHO GTPases Activate ROCKs / postsynaptic actin cytoskeleton / actomyosin structure organization / RHO GTPases activate CIT / Sema4D induced cell migration and growth-cone collapse / muscle filament sliding / myosin complex / myosin II complex / structural constituent of muscle / EPHA-mediated growth cone collapse / microfilament motor activity / myosin heavy chain binding / cleavage furrow / myofibril / mitotic cytokinesis / RHO GTPases activate PAKs / cytoskeletal motor activity / brush border / Smooth Muscle Contraction / skeletal muscle tissue development / RHO GTPases activate PKNs / stress fiber / muscle contraction / positive regulation of protein secretion / neuromuscular junction / ADP binding / RNA stem-loop binding / spindle / mRNA 5'-UTR binding / Z disc / cytoplasmic side of plasma membrane / actin filament binding / regulation of cell shape / lamellipodium / growth cone / virus receptor activity / actin binding / midbody / cell cortex / vesicle / dendritic spine / calmodulin binding / cell adhesion / neuronal cell body / calcium ion binding / symbiont entry into host cell / glutamatergic synapse / cell surface / extracellular exosome / ATP binding / membrane / nucleus / cytoplasm / cytosol
Similarity search - Function
DJBP, EF-hand domain / EF-hand domain / : / IQ calmodulin-binding motif / 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 / : / IQ calmodulin-binding motif / 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 motor domain profile. / Myosin head, motor domain / Myosin head (motor domain) / 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 regulatory light chain 12B / Myosin-10 / Myosin light polypeptide 6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.1 Å
AuthorsHeissler, S.M. / Chinthalapudi, K.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM143539 United States
CitationJournal: Nat Commun / Year: 2026
Title: Structural basis of nonmuscle myosin-2 autoinhibition mechanisms.
Authors: Heissler, S.M. / Grandinetti, G. / Sellers, J.R. / Chinthalapudi, K.
History
DepositionNov 10, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 8, 2026Provider: repository / Type: Initial release
Revision 1.0Jul 8, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jul 8, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jul 8, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 8, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 8, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 8, 2026Data 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: Myosin-10
B: Myosin-10
C: Myosin light polypeptide 6
D: Myosin regulatory light chain 12B
E: Myosin regulatory light chain 12B
F: Myosin light polypeptide 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)533,32012
Polymers532,2276
Non-polymers1,0936
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 3 types, 6 molecules ABCFDE

#1: Protein Myosin-10 / Cellular myosin heavy chain / type B / Myosin heavy chain 10 / Myosin heavy chain / non-muscle IIb ...Cellular myosin heavy chain / type B / Myosin heavy chain 10 / Myosin heavy chain / non-muscle IIb / Non-muscle myosin heavy chain B / NMMHC-B / Non-muscle myosin heavy chain IIb / NMMHC II-b / NMMHC-IIB


Mass: 229361.547 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MYH10 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P35580
#2: Protein Myosin light polypeptide 6 / 17 kDa myosin light chain / LC17 / Myosin light chain 3 / MLC-3 / Myosin light chain alkali 3 / ...17 kDa myosin light chain / LC17 / Myosin light chain 3 / MLC-3 / Myosin light chain alkali 3 / Myosin light chain A3 / Smooth muscle and nonmuscle myosin light chain alkali 6


Mass: 16948.031 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: ELC, MYL6 / Source: (gene. exp.) Homo sapiens (human) / Gene: MYL6 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P60660
#3: Protein Myosin regulatory light chain 12B / MLC-2A / MLC-2 / Myosin regulatory light chain 2-B / smooth muscle isoform / Myosin regulatory ...MLC-2A / MLC-2 / Myosin regulatory light chain 2-B / smooth muscle isoform / Myosin regulatory light chain 20 kDa / MLC20 / Myosin regulatory light chain MRLC2 / SHUJUN-1


Mass: 19804.160 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: The first methionine residue is cleaved after the expression. So the first residue number is serine-1.
Source: (gene. exp.) Homo sapiens (human) / Gene: MYL12B, MRLC2, MYLC2B / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: O14950

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Non-polymers , 3 types, 6 molecules

#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / 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
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: Non-muscle myosin-2B / Type: COMPLEX / Entity ID: #1-#3 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: C-flat-1.2/1.3
VitrificationInstrument: LEICA EM GP / Cryogen name: ETHANE / Humidity: 95 %

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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 defocus max: 3500 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 72 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 QUANTUM (4k x 4k)

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
2SerialEMimage acquisition
4cryoSPARCCTF correction
10cryoSPARCinitial Euler assignment
11cryoSPARCfinal Euler assignment
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 123125 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL

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