9ZN8 | pdb_00009zn8

Structure of rabbit RyR1 complexed with FKBP12.6 and calmodulin in the presence of ATP, ADP, and Mg2+ (mimicking physiological conditions)

PDB DOI: https://doi.org/10.2210/pdb9ZN8/pdb
EM Map EMD-74438: EMDB EMDataResource

Classification: MEMBRANE PROTEIN
Organism(s): Homo sapiens, Oryctolagus cuniculus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2025-12-12 Released: 2026-09-16
Deposition Author(s): Kim, K., Clarke, O.B.
Funding Organization(s): National Institutes of Health/National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIH/NIAMS)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.57 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

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

Literature

Structural identification of the RY12 domain of RyR1 as an ADP sensor and the target of the malignant hyperthermia therapeutic dantrolene

Kim, K., Li, H., Yuan, Q., Melville, Z., Zalk, R., des Georges, A., Frank, J., Hendrickson, W.A., Marks, A.R., Clarke, O.B.

(2026) Nat Commun

DOI: https://doi.org/10.1038/s41467-026-76519-y

Macromolecule Content

Total Structure Weight: 2,379.76 kDa
Atom Count: 146,702
Modeled Residue Count: 18,016
Deposited Residue Count: 21,168
Unique protein chains: 3

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Calmodulin-1	A [auth L], B [auth I], C [auth J], D [auth K]	148	Homo sapiens	Mutation(s): 0 Gene Names: CALM1, CALM, CAM, CAM1
UniProt & NIH Common Fund Data Resources
Find proteins for P0DP23 (Homo sapiens) Explore P0DP23 Go to UniProtKB: P0DP23
PHAROS: P0DP23 GTEx: ENSG00000143933 ENSG00000160014 ENSG00000198668
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0DP23
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptidyl-prolyl cis-trans isomerase FKBP1B	E, J [auth H], K [auth F], L [auth G]	107	Homo sapiens	Mutation(s): 0 Gene Names: FKBP1B, FKBP12.6, FKBP1L, FKBP9, OTK4 EC: 5.2.1.8
UniProt & NIH Common Fund Data Resources
Find proteins for P68106 (Homo sapiens) Explore P68106 Go to UniProtKB: P68106
PHAROS: P68106 GTEx: ENSG00000119782
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P68106
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Ryanodine receptor 1	F [auth A], G [auth C], H [auth D], I [auth B]	5,037	Oryctolagus cuniculus	Mutation(s): 0
UniProt
Find proteins for P11716 (Oryctolagus cuniculus) Explore P11716 Go to UniProtKB: P11716
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P11716
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ATP Query on ATP Download:Ideal Coordinates CCD File SDF format, chain N [auth A] SDF format, chain P [auth C] SDF format, chain R [auth D] SDF format, chain T [auth B] MOL2 format, chain N [auth A] MOL2 format, chain P [auth C] MOL2 format, chain R [auth D] MOL2 format, chain T [auth B] mmCIF format, chain N [auth A] mmCIF format, chain P [auth C] mmCIF format, chain R [auth D] mmCIF format, chain T [auth B]	N [auth A], P [auth C], R [auth D], T [auth B]	ADENOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₃ P₃ ZKHQWZAMYRWXGA-KQYNXXCUSA-N		Interactions Focus chain N [auth A] Focus chain P [auth C] Focus chain R [auth D] Focus chain T [auth B] Interactions & Density Focus chain N [auth A] Focus chain P [auth C] Focus chain R [auth D] Focus chain T [auth B]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain O [auth C] SDF format, chain S [auth B] SDF format, chain Q [auth D] SDF format, chain M [auth A] MOL2 format, chain O [auth C] MOL2 format, chain S [auth B] MOL2 format, chain Q [auth D] MOL2 format, chain M [auth A] mmCIF format, chain O [auth C] mmCIF format, chain S [auth B] mmCIF format, chain Q [auth D] mmCIF format, chain M [auth A]	M [auth A], O [auth C], Q [auth D], S [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain M [auth A] Focus chain O [auth C] Focus chain Q [auth D] Focus chain S [auth B] Interactions & Density Focus chain M [auth A] Focus chain O [auth C] Focus chain Q [auth D] Focus chain S [auth B]