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- PDB-9yrh: Cryo-EM structure of human beta-cardiac myosin bound to omecamtiv... -

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Basic information

Entry
Database: PDB / ID: 9yrh
TitleCryo-EM structure of human beta-cardiac myosin bound to omecamtiv mecarbil in the interacting-heads motif and S2-FH undocked state
Components
  • Myosin light chain 1/3, skeletal muscle isoform
  • Myosin regulatory light chain 11
  • Myosin-7,General control transcription factor GCN4,Enhanced Green fluorescent protein
KeywordsCONTRACTILE PROTEIN / Cardiac Myosin / Interacting Heads Motif / Omecamtiv Mecarbil / Actin Binding
Function / homology
Function and homology information


regulation of slow-twitch skeletal muscle fiber contraction / regulation of the force of skeletal muscle contraction / unconventional myosin complex / Striated Muscle Contraction / contractile muscle fiber / Smooth Muscle Contraction / FCERI mediated MAPK activation / protein localization to nuclear periphery / muscle myosin complex / Activation of the AP-1 family of transcription factors ...regulation of slow-twitch skeletal muscle fiber contraction / regulation of the force of skeletal muscle contraction / unconventional myosin complex / Striated Muscle Contraction / contractile muscle fiber / Smooth Muscle Contraction / FCERI mediated MAPK activation / protein localization to nuclear periphery / muscle myosin complex / Activation of the AP-1 family of transcription factors / negative regulation of ribosomal protein gene transcription by RNA polymerase II / response to amino acid starvation / positive regulation of cellular response to amino acid starvation / mediator complex binding / regulation of the force of heart contraction / transition between fast and slow fiber / myosin filament / Oxidative Stress Induced Senescence / cardiac muscle hypertrophy in response to stress / muscle filament sliding / adult heart development / myosin complex / myosin II complex / structural constituent of muscle / ventricular cardiac muscle tissue morphogenesis / microfilament motor activity / myofibril / cytoskeletal motor activity / TFIID-class transcription factor complex binding / amino acid biosynthetic process / positive regulation of RNA polymerase II transcription preinitiation complex assembly / positive regulation of transcription initiation by RNA polymerase II / ATP metabolic process / skeletal muscle tissue development / striated muscle contraction / skeletal muscle contraction / cardiac muscle contraction / stress fiber / cellular response to nutrient levels / regulation of heart rate / muscle contraction / cellular response to amino acid starvation / bioluminescence / sarcomere / generation of precursor metabolites and energy / RNA polymerase II transcription regulator complex / Z disc / actin filament binding / DNA-binding transcription activator activity, RNA polymerase II-specific / transcription regulator complex / sequence-specific DNA binding / RNA polymerase II-specific DNA-binding transcription factor binding / DNA-binding transcription factor activity, RNA polymerase II-specific / calmodulin binding / intracellular signal transduction / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / calcium ion binding / chromatin binding / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / ATP binding / identical protein binding / nucleus / cytoplasm
Similarity search - Function
: / EF-hand domain / : / Basic region leucine zipper / DNA repair protein XRCC4-like, C-terminal / Myosin tail / Myosin tail / Myosin N-terminal SH3-like domain / Myosin S1 fragment, N-terminal / Basic-leucine zipper (bZIP) domain signature. ...: / EF-hand domain / : / Basic region leucine zipper / DNA repair protein XRCC4-like, C-terminal / Myosin tail / Myosin tail / Myosin N-terminal SH3-like domain / Myosin S1 fragment, N-terminal / Basic-leucine zipper (bZIP) domain signature. / Basic-leucine zipper (bZIP) domain profile. / basic region leucin zipper / Basic-leucine zipper domain / Basic-leucine zipper domain superfamily / 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 / : / Green fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / 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
Chem-2OW / ADENOSINE-5'-DIPHOSPHATE / PHOSPHATE ION / General control transcription factor GCN4 / Myosin light chain 1/3, skeletal muscle isoform / Myosin-7 / Green fluorescent protein / Myosin regulatory light chain 11
Similarity search - Component
Biological speciesHomo sapiens (human)
Saccharomyces cerevisiae (brewer's yeast)
Aequorea victoria (jellyfish)
Mus musculus (house mouse)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsSomavarapu, A.K. / Craig, R. / Padron, R.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)HL164560 United States
National Institutes of Health/National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIH/NIAMS)AR081941 United States
CitationJournal: To Be Published
Title: Cryo-EM Reveals How Cardiomyopathy Therapeutic Drugs Modulate the Myosin Motors of the Heart
Authors: Somavarapu, A.K. / Ge, J. / Yengo, C.M. / Craig, R. / Padron, R.
History
DepositionOct 16, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 8, 2026Provider: repository / Type: Initial release
Revision 1.0Apr 8, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Apr 8, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Apr 8, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 8, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 8, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Apr 8, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Apr 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

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Assembly

Deposited unit
A: Myosin-7,General control transcription factor GCN4,Enhanced Green fluorescent protein
B: Myosin-7,General control transcription factor GCN4,Enhanced Green fluorescent protein
C: Myosin light chain 1/3, skeletal muscle isoform
D: Myosin light chain 1/3, skeletal muscle isoform
E: Myosin regulatory light chain 11
F: Myosin regulatory light chain 11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)382,35812
Polymers380,5116
Non-polymers1,8476
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 ABCDEF

#1: Protein Myosin-7,General control transcription factor GCN4,Enhanced Green fluorescent protein / Myosin heavy chain 7 / Myosin heavy chain slow isoform / MyHC-slow / Myosin heavy chain / cardiac ...Myosin heavy chain 7 / Myosin heavy chain slow isoform / MyHC-slow / Myosin heavy chain / cardiac muscle beta isoform / MyHC-beta / Amino acid biosynthesis regulatory protein / General control protein GCN4


Mass: 150656.500 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Saccharomyces cerevisiae (brewer's yeast), (gene. exp.) Aequorea victoria (jellyfish)
Gene: MYH7, MYHCB, GCN4, AAS101, AAS3, ARG9, YEL009C, GFP / Production host: Mus musculus (house mouse)
References: UniProt: P12883, UniProt: P03069, UniProt: P42212
#2: Protein Myosin light chain 1/3, skeletal muscle isoform / MLC1/MLC3 / MLC1F/MLC3F / Myosin light chain alkali 1/2 / Myosin light chain A1/A2


Mass: 20620.490 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P05977
#3: Protein Myosin regulatory light chain 11 / Fast skeletal myosin light chain 2 / MLC2F / Myosin light chain 11 / Myosin regulatory light chain ...Fast skeletal myosin light chain 2 / MLC2F / Myosin light chain 11 / Myosin regulatory light chain 2 / skeletal muscle isoform


Mass: 18978.445 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P97457

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Non-polymers , 3 types, 6 molecules

#4: Chemical ChemComp-2OW / methyl 4-(2-fluoro-3-{[(6-methylpyridin-3-yl)carbamoyl]amino}benzyl)piperazine-1-carboxylate / omecamtiv mercarbil


Mass: 401.435 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H24FN5O3 / Feature type: SUBJECT OF INVESTIGATION
#5: 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
#6: Chemical ChemComp-PO4 / PHOSPHATE ION


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

Component
IDNameTypeEntity IDParent-IDSource
1Human beta-cardiac myosin bound to omecamtiv mecarbil in the interacting-heads motif and S2-FH undocked stateCOMPLEX#1-#30MULTIPLE SOURCES
2Myosin-7COMPLEX#11RECOMBINANT
3Myosin light chain 1/3 and Myosin regulatory light chain 11COMPLEX#2-#31NATURAL
Molecular weightValue: 0.11652168 MDa / Experimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
22Homo sapiens (human)9606
33Mus musculus (house mouse)10090
Source (recombinant)Organism: Mus musculus (house mouse)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid type: UltrAuFoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen 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 defocus max: 2000 nm / Nominal defocus min: 1000 nm
Specimen holderSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 49.5 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategoryFitting-ID
1cryoSPARCparticle selection
2Topazparticle selection
5cryoSPARCCTF correction
8UCSF ChimeraXmodel fitting1
9MDFFmodel fitting1
10Cootmodel fitting1
12PHENIX1.20.1_4487:model refinement1
13PHENIX1.20.1_4487:model refinement2
14cryoSPARCinitial Euler assignment
15cryoSPARCfinal Euler assignment
16cryoSPARCclassification
17cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 82127 / Symmetry type: POINT
Atomic model building
IDProtocolSpace
1FLEXIBLE FITREAL
2
Atomic model building

Source name: PDB / Type: experimental model

IDPDB-ID 3D fitting-IDAccession codeChain residue rangeInitial refinement model-IDPdb chain residue range
18ACT

8act

18ACT4-87514-875
22FXM

2fxm

22FXM838-9432838-943
RefinementHighest resolution: 3.8 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00320094
ELECTRON MICROSCOPYf_angle_d0.63927032
ELECTRON MICROSCOPYf_dihedral_angle_d5.3642664
ELECTRON MICROSCOPYf_chiral_restr0.0382912
ELECTRON MICROSCOPYf_plane_restr0.0053519

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