9YK9 | pdb_00009yk9

The structure of the cardiac native crossbridge in the rigor state, myosin heads bound to actin molecules 1 and 2

PDB DOI: https://doi.org/10.2210/pdb9YK9/pdb
EM Map EMD-73042: EMDB EMDataResource

Classification: MOTOR PROTEIN
Organism(s): Sus scrofa
Mutation(s): No

Deposited: 2025-10-06 Released: 2026-07-22
Deposition Author(s): Galkin, V.E., Risi, C.M.
Funding Organization(s): National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 4.50 Å
Aggregation State: FILAMENT
Reconstruction Method: SINGLE PARTICLE

Starting Models: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

The structure of the native cardiac cross-bridge

Galkin, V.E., Risi, C.M.

To be published.

Macromolecule Content

Total Structure Weight: 825.93 kDa
Atom Count: 30,678
Modeled Residue Count: 3,843
Deposited Residue Count: 7,191
Unique protein chains: 5

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Actin, alpha cardiac muscle 1	A, B, C, D	377	Sus scrofa	Mutation(s): 0
UniProt
Find proteins for B6VNT8 (Sus scrofa) Explore B6VNT8 Go to UniProtKB: B6VNT8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	B6VNT8
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Tropomyosin alpha-1 chain	E, F, G, H	284	Sus scrofa	Mutation(s): 0
UniProt
Find proteins for P42639 (Sus scrofa) Explore P42639 Go to UniProtKB: P42639
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P42639
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Troponin T2, cardiac type	I	285	Sus scrofa	Mutation(s): 0
UniProt
Find proteins for A0A5G2Q8N0 (Sus scrofa) Explore A0A5G2Q8N0 Go to UniProtKB: A0A5G2Q8N0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A5G2Q8N0
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Myosin-7	J, K	1,935	Sus scrofa	Mutation(s): 0
UniProt
Find proteins for P79293 (Sus scrofa) Explore P79293 Go to UniProtKB: P79293
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P79293
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Myosin light chain 3	L, M	196	Sus scrofa	Mutation(s): 0
UniProt
Find proteins for F1SNW4 (Sus scrofa) Explore F1SNW4 Go to UniProtKB: F1SNW4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	F1SNW4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ADP Query on ADP Download:Ideal Coordinates CCD File SDF format, chain T [auth D] SDF format, chain R [auth C] SDF format, chain P [auth B] SDF format, chain N [auth A] MOL2 format, chain T [auth D] MOL2 format, chain R [auth C] MOL2 format, chain P [auth B] MOL2 format, chain N [auth A] mmCIF format, chain T [auth D] mmCIF format, chain R [auth C] mmCIF format, chain P [auth B] mmCIF format, chain N [auth A]	N [auth A], P [auth B], R [auth C], T [auth D]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain N [auth A] Focus chain P [auth B] Focus chain R [auth C] Focus chain T [auth D] Interactions & Density Focus chain N [auth A] Focus chain P [auth B] Focus chain R [auth C] Focus chain T [auth D]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain U [auth D] SDF format, chain S [auth C] SDF format, chain Q [auth B] SDF format, chain O [auth A] MOL2 format, chain U [auth D] MOL2 format, chain S [auth C] MOL2 format, chain Q [auth B] MOL2 format, chain O [auth A] mmCIF format, chain U [auth D] mmCIF format, chain S [auth C] mmCIF format, chain Q [auth B] mmCIF format, chain O [auth A]	O [auth A], Q [auth B], S [auth C], U [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain O [auth A] Focus chain Q [auth B] Focus chain S [auth C] Focus chain U [auth D] Interactions & Density Focus chain O [auth A] Focus chain Q [auth B] Focus chain S [auth C] Focus chain U [auth D]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 4.50 Å
Aggregation State: FILAMENT
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX
RECONSTRUCTION	RELION	3.1

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2026-07-22

Deposition Author(s):

Galkin, V.E.

Risi, C.M.

Funding Organization	Location	Grant Number
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)	United States	R01HL160966
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01GM120137