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- PDB-9z40: Cryo-EM structure of full-length human NM2B -

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Basic information

Entry
Database: PDB / ID: 9z40
TitleCryo-EM structure of full-length human NM2B
Components
  • Myosin light polypeptide 6
  • Myosin regulatory light chain 12B
  • Myosin-10
KeywordsMOTOR PROTEIN / ATPase enzyme
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: 10 Å
AuthorsHeissler, S.M. / Chinthalapudi, K.C.
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: Sarah M Heissler / Giovanna Grandinetti / James R Sellers / Krishna Chinthalapudi /
Abstract: Nonmuscle myosin-2 (NM2) is a fundamental actin-based mechanochemical ATPase that regulates cellular architecture, migration, adhesion, and force generation across diverse biological contexts. NM2 ...Nonmuscle myosin-2 (NM2) is a fundamental actin-based mechanochemical ATPase that regulates cellular architecture, migration, adhesion, and force generation across diverse biological contexts. NM2 function is tightly regulated by a structural transition between an autoinhibited monomeric (10S) conformation in which ATPase activity, actin binding, and filament assembly are coordinately suppressed and an enzymatically active, filamentous conformation. The autoinhibited conformation is critical for the spatial and temporal control of contractility in nonmuscle cells, yet structural insights into the 10S conformation remain largely elusive. Here, we report a ~53-nm elongated full-length structure of NM2B in the 10S conformation and four distinct cryo-EM structures representing the conformational landscape within the human NM2B 10S state. These structures reveal a tri-segmented tail fold that sequesters interfaces essential for actin binding and filament assembly. The asymmetric arrangement of myosin heavy and light chains provides a mechanistic foundation for understanding how regulatory post-translational modifications and disease-associated mutations shift NM2 conformational equilibria and may enable the development of structure-based interventions for cytoskeletal diseases including hearing loss, neurodegeneration, and cancer.
History
DepositionNov 8, 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: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Jul 8, 2026Data content type: Additional map / Part number: 2 / Data content type: Additional 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 / 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: RLC / 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 modificationY

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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: Nonmuscle 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
VitrificationCryogen name: ETHANE

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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: 130000 X / Nominal defocus max: 3500 nm / Nominal defocus min: 1500 nm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 72 e/Å2 / Film or detector model: GATAN K2 QUANTUM (4k x 4k)
EM imaging opticsEnergyfilter slit width: 20 eV

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
2SerialEMimage acquisition
9PHENIXmodel refinement
11cryoSPARCfinal Euler assignment
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 10 Å / Resolution method: OTHER / Num. of particles: 38939
Details: It is a composite map of the head and tail domains.
Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT
Atomic model buildingDetails: 7MF3 and AlphaFold / Source name: Other / Type: other
RefinementHighest resolution: 10 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00436036
ELECTRON MICROSCOPYf_angle_d0.68948262
ELECTRON MICROSCOPYf_dihedral_angle_d12.59214341
ELECTRON MICROSCOPYf_chiral_restr0.0395270
ELECTRON MICROSCOPYf_plane_restr0.0056414

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