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- PDB-9ykn: The structure of the cardiac native crossbridge in the rigor stat... -

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Basic information

Entry
Database: PDB / ID: 9ykn
TitleThe structure of the cardiac native crossbridge in the rigor state, myosin heads with essential and regulatory light chains bound to actin molecules 6 and 7
Components
  • Actin, alpha cardiac muscle 1
  • MYL2
  • Myosin light chain 3
  • Myosin-7
  • Tropomyosin alpha-1 chain
  • Troponin T2, cardiac type
KeywordsMOTOR PROTEIN / cardiac myosin / tropomyosin / thin filament / troponin
Function / homology
Function and homology information


muscle cell fate specification / RHOB GTPase cycle / Striated Muscle Contraction / RHOA GTPase cycle / Regulation of CDH1 Function / Formation of the dystrophin-glycoprotein complex (DGC) / regulation of striated muscle contraction / cardiac myofibril / regulation of the force of heart contraction / troponin complex ...muscle cell fate specification / RHOB GTPase cycle / Striated Muscle Contraction / RHOA GTPase cycle / Regulation of CDH1 Function / Formation of the dystrophin-glycoprotein complex (DGC) / regulation of striated muscle contraction / cardiac myofibril / regulation of the force of heart contraction / troponin complex / actin-myosin filament sliding / A band / regulation of muscle contraction / adult heart development / myosin filament / muscle filament sliding / myosin complex / myosin II complex / I band / heart contraction / structural constituent of muscle / ventricular cardiac muscle tissue morphogenesis / myosin binding / microfilament motor activity / positive regulation of the force of heart contraction / mesenchyme migration / myofibril / cytoskeletal motor activity / actin monomer binding / cardiac muscle contraction / actin filament organization / sarcomere / filopodium / actin filament / negative regulation of cell growth / structural constituent of cytoskeleton / heart development / actin filament binding / actin cytoskeleton / lamellipodium / cell body / calmodulin binding / protein heterodimerization activity / positive regulation of gene expression / calcium ion binding / protein homodimerization activity / ATP binding / identical protein binding / cytosol / cytoplasm
Similarity search - Function
Troponin T / : / Troponin / Troponin domain superfamily / Troponin / Tropomyosins signature. / Tropomyosin / Tropomyosin / DNA repair protein XRCC4-like, C-terminal / Myosin tail ...Troponin T / : / Troponin / Troponin domain superfamily / Troponin / Tropomyosins signature. / Tropomyosin / Tropomyosin / DNA repair protein XRCC4-like, C-terminal / 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. / Myosin motor domain profile. / Myosin head, motor domain / Myosin head (motor domain) / Myosin. Large ATPases. / IQ motif profile. / Kinesin motor domain superfamily / : / Actins signature 1. / Actin, conserved site / Actins signature 2. / Actin/actin-like conserved site / Actins and actin-related proteins signature. / Actin / Actin family / Actin / EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / ATPase, nucleotide 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 / Troponin T, cardiac muscle / Actin, alpha cardiac muscle 1 / Myosin light chain 3 / Tropomyosin alpha-1 chain / Myosin-7 / MYL2
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 5.3 Å
AuthorsGalkin, V.E. / Risi, C.M.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)R01HL160966 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM120137 United States
CitationJournal: To Be Published
Title: The structure of the native cardiac cross-bridge
Authors: Galkin, V.E. / Risi, C.M.
History
DepositionOct 7, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 22, 2026Provider: repository / Type: Initial release
Revision 1.0Jul 22, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jul 22, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jul 22, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 22, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 22, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 22, 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: Actin, alpha cardiac muscle 1
B: Actin, alpha cardiac muscle 1
C: Tropomyosin alpha-1 chain
D: Tropomyosin alpha-1 chain
E: Tropomyosin alpha-1 chain
F: Tropomyosin alpha-1 chain
G: Troponin T2, cardiac type
H: Myosin-7
I: Myosin-7
J: Myosin light chain 3
K: Myosin light chain 3
L: MYL2
M: MYL2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)778,73217
Polymers777,82913
Non-polymers9034
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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Protein , 6 types, 13 molecules ABCDEFGHIJKLM

#1: Protein Actin, alpha cardiac muscle 1 / Cardiac muscle alpha actin 1


Mass: 42064.891 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: B6VNT8
#2: Protein
Tropomyosin alpha-1 chain / Alpha-tropomyosin / Tropomyosin-1


Mass: 32762.656 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: P42639
#3: Protein Troponin T2, cardiac type


Mass: 33941.738 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A5G2Q8N0
#4: Protein Myosin-7 / 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


Mass: 223649.094 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: P79293
#5: Protein Myosin light chain 3 / Myosin light chain 1 / slow-twitch muscle B/ventricular isoform


Mass: 21788.875 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1SNW4
#6: Protein MYL2 / Myosin light chain 2 / Myosin regulatory light chain 2 / ventricular/cardiac muscle isoform / ...Myosin light chain 2 / Myosin regulatory light chain 2 / ventricular/cardiac muscle isoform / Myosin regulatory light chain ventricular isoform


Mass: 18915.363 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: Q8MHY0

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Non-polymers , 2 types, 4 molecules

#7: 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
#8: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg

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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: FILAMENT / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: complex of heavy meromyosin bound to cardiac thin filament
Type: COMPLEX / Entity ID: #1-#6 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Sus scrofa (pig)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: EMS Lacey Carbon
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 278 K

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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: 500 nm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 34 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 10
Details: Images were collected in a movie mode, 40 frames, with a dose of 0.85 e/A2 per frame

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Processing

EM software
IDNameVersionCategory
1RELION3.1particle selection
2EPUimage acquisition
4CTFFIND4CTF correction
7PHENIXmodel fitting
8ISOLDEmodel fitting
9MDFFmodel fitting
10UCSF Chimeramodel fitting
12PHENIXmodel refinement
13RELION3.1initial Euler assignment
14RELION3.1final Euler assignment
15RELION3.1classification
16RELION3.13D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 5235506
3D reconstructionResolution: 5.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 17875 / Algorithm: BACK PROJECTION / Details: map filtered to 6.0 A / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Atomic model building
IDPDB-ID 3D fitting-IDAccession codeInitial refinement model-IDSource nameType
17JH7

7jh7

17JH71PDBexperimental model
25H53

5h53

15H532PDBexperimental model
38DD0

8dd0

18DD03PDBexperimental model
46SFA

6sfa

16SFA4PDBexperimental model
57KO5

7ko5

17KO55PDBexperimental model

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