9ZND | pdb_00009znd

Structure of rabbit RyR1 complexed with FKBP12.6 and calmodulin in the presence of dantrolene, ATP, 4-chloro-m-cresol, caffeine, and Mg2+

PDB DOI: https://doi.org/10.2210/pdb9ZND/pdb
EM Map EMD-74445: 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: 3.09 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: 2,388.15 kDa
Atom Count: 143,134
Modeled Residue Count: 18,068
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
Peptidyl-prolyl cis-trans isomerase FKBP1B	A [auth E], B [auth F], C [auth G], D [auth H]	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

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Calmodulin-1	E [auth I], F [auth J], G [auth K], H [auth L]	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: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Ryanodine receptor 1	I [auth D], J [auth B], K [auth A], L [auth C]	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 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CPS Query on CPS Download:Ideal Coordinates CCD File SDF format, chain ZA [auth C] SDF format, chain V [auth D] SDF format, chain PA [auth A] SDF format, chain FA [auth B] MOL2 format, chain ZA [auth C] MOL2 format, chain V [auth D] MOL2 format, chain PA [auth A] MOL2 format, chain FA [auth B] mmCIF format, chain ZA [auth C] mmCIF format, chain V [auth D] mmCIF format, chain PA [auth A] mmCIF format, chain FA [auth B]	FA [auth B], PA [auth A], V [auth D], ZA [auth C]	3-[(3-CHOLAMIDOPROPYL)DIMETHYLAMMONIO]-1-PROPANESULFONATE C₃₂ H₅₈ N₂ O₇ S UMCMPZBLKLEWAF-BCTGSCMUSA-N		Interactions Focus chain FA [auth B] Focus chain PA [auth A] Focus chain V [auth D] Focus chain ZA [auth C] Interactions & Density Focus chain FA [auth B] Focus chain PA [auth A] Focus chain V [auth D] Focus chain ZA [auth C]
ATP (Subject of Investigation/LOI) Query on ATP Download:Ideal Coordinates CCD File SDF format, chain XA [auth C] SDF format, chain WA [auth C] SDF format, chain T [auth D] SDF format, chain S [auth D] SDF format, chain NA [auth A] SDF format, chain MA [auth A] SDF format, chain DA [auth B] SDF format, chain CA [auth B] MOL2 format, chain XA [auth C] MOL2 format, chain WA [auth C] MOL2 format, chain T [auth D] MOL2 format, chain S [auth D] MOL2 format, chain NA [auth A] MOL2 format, chain MA [auth A] MOL2 format, chain DA [auth B] MOL2 format, chain CA [auth B] mmCIF format, chain XA [auth C] mmCIF format, chain WA [auth C] mmCIF format, chain T [auth D] mmCIF format, chain S [auth D] mmCIF format, chain NA [auth A] mmCIF format, chain MA [auth A] mmCIF format, chain DA [auth B] mmCIF format, chain CA [auth B]	CA [auth B] DA [auth B] MA [auth A] NA [auth A] S [auth D] CA [auth B], DA [auth B], MA [auth A], NA [auth A], S [auth D], T [auth D], WA [auth C], XA [auth C]	ADENOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₃ P₃ ZKHQWZAMYRWXGA-KQYNXXCUSA-N		Interactions Focus chain CA [auth B] Focus chain DA [auth B] Focus chain MA [auth A] Focus chain NA [auth A] Focus chain S [auth D] Focus chain T [auth D] Focus chain WA [auth C] Focus chain XA [auth C] Interactions & Density Focus chain CA [auth B] Focus chain DA [auth B] Focus chain MA [auth A] Focus chain NA [auth A] Focus chain S [auth D] Focus chain T [auth D] Focus chain WA [auth C] Focus chain XA [auth C]
U1C (Subject of Investigation/LOI) Query on U1C Download:Ideal Coordinates CCD File SDF format, chain Y [auth B] SDF format, chain SA [auth C] SDF format, chain O [auth D] SDF format, chain IA [auth A] MOL2 format, chain Y [auth B] MOL2 format, chain SA [auth C] MOL2 format, chain O [auth D] MOL2 format, chain IA [auth A] mmCIF format, chain Y [auth B] mmCIF format, chain SA [auth C] mmCIF format, chain O [auth D] mmCIF format, chain IA [auth A]	IA [auth A], O [auth D], SA [auth C], Y [auth B]	Dantrolene C₁₄ H₁₀ N₄ O₅ OZOMQRBLCMDCEG-CHHVJCJISA-N		Interactions Focus chain IA [auth A] Focus chain O [auth D] Focus chain SA [auth C] Focus chain Y [auth B] Interactions & Density Focus chain IA [auth A] Focus chain O [auth D] Focus chain SA [auth C] Focus chain Y [auth B]
CFF Query on CFF Download:Ideal Coordinates CCD File SDF format, chain YA [auth C] SDF format, chain U [auth D] SDF format, chain OA [auth A] SDF format, chain EA [auth B] MOL2 format, chain YA [auth C] MOL2 format, chain U [auth D] MOL2 format, chain OA [auth A] MOL2 format, chain EA [auth B] mmCIF format, chain YA [auth C] mmCIF format, chain U [auth D] mmCIF format, chain OA [auth A] mmCIF format, chain EA [auth B]	EA [auth B], OA [auth A], U [auth D], YA [auth C]	CAFFEINE C₈ H₁₀ N₄ O₂ RYYVLZVUVIJVGH-UHFFFAOYSA-N		Interactions Focus chain EA [auth B] Focus chain OA [auth A] Focus chain U [auth D] Focus chain YA [auth C] Interactions & Density Focus chain EA [auth B] Focus chain OA [auth A] Focus chain U [auth D] Focus chain YA [auth C]
43M (Subject of Investigation/LOI) Query on 43M Download:Ideal Coordinates CCD File SDF format, chain Z [auth B] SDF format, chain VA [auth C] SDF format, chain UA [auth C] SDF format, chain TA [auth C] SDF format, chain R [auth D] SDF format, chain Q [auth D] SDF format, chain P [auth D] SDF format, chain LA [auth A] SDF format, chain KA [auth A] SDF format, chain JA [auth A] SDF format, chain BA [auth B] SDF format, chain AA [auth B] MOL2 format, chain Z [auth B] MOL2 format, chain VA [auth C] MOL2 format, chain UA [auth C] MOL2 format, chain TA [auth C] MOL2 format, chain R [auth D] MOL2 format, chain Q [auth D] MOL2 format, chain P [auth D] MOL2 format, chain LA [auth A] MOL2 format, chain KA [auth A] MOL2 format, chain JA [auth A] MOL2 format, chain BA [auth B] MOL2 format, chain AA [auth B] mmCIF format, chain Z [auth B] mmCIF format, chain VA [auth C] mmCIF format, chain UA [auth C] mmCIF format, chain TA [auth C] mmCIF format, chain R [auth D] mmCIF format, chain Q [auth D] mmCIF format, chain P [auth D] mmCIF format, chain LA [auth A] mmCIF format, chain KA [auth A] mmCIF format, chain JA [auth A] mmCIF format, chain BA [auth B] mmCIF format, chain AA [auth B]	AA [auth B] BA [auth B] JA [auth A] KA [auth A] LA [auth A] AA [auth B], BA [auth B], JA [auth A], KA [auth A], LA [auth A], P [auth D], Q [auth D], R [auth D], TA [auth C], UA [auth C], VA [auth C], Z [auth B]	4-CHLORO-3-METHYLPHENOL C₇ H₇ Cl O CFKMVGJGLGKFKI-UHFFFAOYSA-N		Interactions Focus chain AA [auth B] Focus chain BA [auth B] Focus chain JA [auth A] Focus chain KA [auth A] Focus chain LA [auth A] Focus chain P [auth D] Focus chain Q [auth D] Focus chain R [auth D] Focus chain TA [auth C] Focus chain UA [auth C] Focus chain VA [auth C] Focus chain Z [auth B] Interactions & Density Focus chain AA [auth B] Focus chain BA [auth B] Focus chain JA [auth A] Focus chain KA [auth A] Focus chain LA [auth A] Focus chain P [auth D] Focus chain Q [auth D] Focus chain R [auth D] Focus chain TA [auth C] Focus chain UA [auth C] Focus chain VA [auth C] Focus chain Z [auth B]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain X [auth B] SDF format, chain RA [auth C] SDF format, chain N [auth D] SDF format, chain HA [auth A] MOL2 format, chain X [auth B] MOL2 format, chain RA [auth C] MOL2 format, chain N [auth D] MOL2 format, chain HA [auth A] mmCIF format, chain X [auth B] mmCIF format, chain RA [auth C] mmCIF format, chain N [auth D] mmCIF format, chain HA [auth A]	HA [auth A], N [auth D], RA [auth C], X [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain HA [auth A] Focus chain N [auth D] Focus chain RA [auth C] Focus chain X [auth B] Interactions & Density Focus chain HA [auth A] Focus chain N [auth D] Focus chain RA [auth C] Focus chain X [auth B]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain W [auth B] SDF format, chain QA [auth C] SDF format, chain M [auth D] SDF format, chain GA [auth A] MOL2 format, chain W [auth B] MOL2 format, chain QA [auth C] MOL2 format, chain M [auth D] MOL2 format, chain GA [auth A] mmCIF format, chain W [auth B] mmCIF format, chain QA [auth C] mmCIF format, chain M [auth D] mmCIF format, chain GA [auth A]	GA [auth A], M [auth D], QA [auth C], W [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain GA [auth A] Focus chain M [auth D] Focus chain QA [auth C] Focus chain W [auth B] Interactions & Density Focus chain GA [auth A] Focus chain M [auth D] Focus chain QA [auth C] Focus chain W [auth B]