9S4N | pdb_00009s4n

Activated-state RyR1 with activating ligand mixture (Calcium/ACP/Caffeine) in the native membrane

PDB DOI: https://doi.org/10.2210/pdb9S4N/pdb
EM Map EMD-54570: EMDB EMDataResource

Classification: MEMBRANE PROTEIN
Organism(s): Oryctolagus cuniculus
Mutation(s): No

Deposited: 2025-07-28 Released: 2026-08-12
Deposition Author(s): Mikirtumov, V.
Funding Organization(s): German Research Foundation (DFG), Helmholtz Association

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.53 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Activation of RyR1 in native membranes

Mikirtumov, V., Golusik, S., Sprink, T., Balyschew, N., Yang, W., Kotecha, A., Kudryashev, M.

To be published.

Macromolecule Content

Total Structure Weight: 2,320.81 kDa
Atom Count: 144,284
Modeled Residue Count: 18,044
Deposited Residue Count: 20,580
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ryanodine receptor 1	A, B, C, D	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

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptidyl-prolyl cis-trans isomerase FKBP1A	E, F, G, H	108	Oryctolagus cuniculus	Mutation(s): 0 EC: 5.2.1.8
UniProt
Find proteins for P62943 (Oryctolagus cuniculus) Explore P62943 Go to UniProtKB: P62943
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P62943
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
POV (Subject of Investigation/LOI) Query on POV Download:Ideal Coordinates CCD File SDF format, chain Z [auth C] SDF format, chain U [auth B] SDF format, chain T [auth B] SDF format, chain O [auth A] SDF format, chain N [auth A] SDF format, chain M [auth A] SDF format, chain FA [auth D] SDF format, chain AA [auth C] MOL2 format, chain Z [auth C] MOL2 format, chain U [auth B] MOL2 format, chain T [auth B] MOL2 format, chain O [auth A] MOL2 format, chain N [auth A] MOL2 format, chain M [auth A] MOL2 format, chain FA [auth D] MOL2 format, chain AA [auth C] mmCIF format, chain Z [auth C] mmCIF format, chain U [auth B] mmCIF format, chain T [auth B] mmCIF format, chain O [auth A] mmCIF format, chain N [auth A] mmCIF format, chain M [auth A] mmCIF format, chain FA [auth D] mmCIF format, chain AA [auth C]	AA [auth C] FA [auth D] M [auth A] N [auth A] O [auth A] AA [auth C], FA [auth D], M [auth A], N [auth A], O [auth A], T [auth B], U [auth B], Z [auth C]	(2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate C₄₂ H₈₂ N O₈ P WTJKGGKOPKCXLL-PFDVCBLKSA-N		Interactions Focus chain AA [auth C] Focus chain FA [auth D] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain T [auth B] Focus chain U [auth B] Focus chain Z [auth C] Interactions & Density Focus chain AA [auth C] Focus chain FA [auth D] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain T [auth B] Focus chain U [auth B] Focus chain Z [auth C]
ACP (Subject of Investigation/LOI) Query on ACP Download:Ideal Coordinates CCD File SDF format, chain X [auth C] SDF format, chain R [auth B] SDF format, chain K [auth A] SDF format, chain DA [auth D] MOL2 format, chain X [auth C] MOL2 format, chain R [auth B] MOL2 format, chain K [auth A] MOL2 format, chain DA [auth D] mmCIF format, chain X [auth C] mmCIF format, chain R [auth B] mmCIF format, chain K [auth A] mmCIF format, chain DA [auth D]	DA [auth D], K [auth A], R [auth B], X [auth C]	PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER C₁₁ H₁₈ N₅ O₁₂ P₃ UFZTZBNSLXELAL-IOSLPCCCSA-N		Interactions Focus chain DA [auth D] Focus chain K [auth A] Focus chain R [auth B] Focus chain X [auth C] Interactions & Density Focus chain DA [auth D] Focus chain K [auth A] Focus chain R [auth B] Focus chain X [auth C]
CFF (Subject of Investigation/LOI) Query on CFF Download:Ideal Coordinates CCD File SDF format, chain Y [auth C] SDF format, chain S [auth B] SDF format, chain L [auth A] SDF format, chain EA [auth D] MOL2 format, chain Y [auth C] MOL2 format, chain S [auth B] MOL2 format, chain L [auth A] MOL2 format, chain EA [auth D] mmCIF format, chain Y [auth C] mmCIF format, chain S [auth B] mmCIF format, chain L [auth A] mmCIF format, chain EA [auth D]	EA [auth D], L [auth A], S [auth B], Y [auth C]	CAFFEINE C₈ H₁₀ N₄ O₂ RYYVLZVUVIJVGH-UHFFFAOYSA-N		Interactions Focus chain EA [auth D] Focus chain L [auth A] Focus chain S [auth B] Focus chain Y [auth C] Interactions & Density Focus chain EA [auth D] Focus chain L [auth A] Focus chain S [auth B] Focus chain Y [auth C]
ZN (Subject of Investigation/LOI) Query on ZN Download:Ideal Coordinates CCD File SDF format, chain V [auth C] SDF format, chain P [auth B] SDF format, chain I [auth A] SDF format, chain BA [auth D] MOL2 format, chain V [auth C] MOL2 format, chain P [auth B] MOL2 format, chain I [auth A] MOL2 format, chain BA [auth D] mmCIF format, chain V [auth C] mmCIF format, chain P [auth B] mmCIF format, chain I [auth A] mmCIF format, chain BA [auth D]	BA [auth D], I [auth A], P [auth B], V [auth C]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain BA [auth D] Focus chain I [auth A] Focus chain P [auth B] Focus chain V [auth C] Interactions & Density Focus chain BA [auth D] Focus chain I [auth A] Focus chain P [auth B] Focus chain V [auth C]
CA (Subject of Investigation/LOI) Query on CA Download:Ideal Coordinates CCD File SDF format, chain W [auth C] SDF format, chain Q [auth B] SDF format, chain J [auth A] SDF format, chain CA [auth D] MOL2 format, chain W [auth C] MOL2 format, chain Q [auth B] MOL2 format, chain J [auth A] MOL2 format, chain CA [auth D] mmCIF format, chain W [auth C] mmCIF format, chain Q [auth B] mmCIF format, chain J [auth A] mmCIF format, chain CA [auth D]	CA [auth D], J [auth A], Q [auth B], W [auth C]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain CA [auth D] Focus chain J [auth A] Focus chain Q [auth B] Focus chain W [auth C] Interactions & Density Focus chain CA [auth D] Focus chain J [auth A] Focus chain Q [auth B] Focus chain W [auth C]