9YJV | pdb_00009yjv

Structure of RyR1-toxin complex

PDB DOI: https://doi.org/10.2210/pdb9YJV/pdb
EM Map EMD-73036: EMDB EMDataResource

Classification: TRANSPORT PROTEIN/ISOMERASE/TOXIN
Organism(s): Oryctolagus cuniculus, Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2025-10-05 Released: 2026-10-07
Deposition Author(s): Zhang, Y., Yuchi, Z., Van Petegem, F.
Funding Organization(s): Canadian Institutes of Health Research (CIHR), Chinese Scholarship Council

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.87 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

Validation slider image for 9YJV

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

Literature

Structure of RyR1-toxin complex

Zhang, Y., Yuchi, Z., Van Petegem, F.

To be published.

Macromolecule Content

Total Structure Weight: 2,314.84 kDa
Atom Count: 124,751
Modeled Residue Count: 16,816
Deposited Residue Count: 20,576
Unique protein chains: 2

Macromolecules

Find similar proteins by:

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

Find similar proteins by:

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptidyl-prolyl cis-trans isomerase FKBP1B	B, C, E, 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

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ATP Query on ATP Download:Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain N [auth D] SDF format, chain S [auth F] SDF format, chain Y [auth H] MOL2 format, chain I [auth A] MOL2 format, chain N [auth D] MOL2 format, chain S [auth F] MOL2 format, chain Y [auth H] mmCIF format, chain I [auth A] mmCIF format, chain N [auth D] mmCIF format, chain S [auth F] mmCIF format, chain Y [auth H]	I [auth A], N [auth D], S [auth F], Y [auth H]	ADENOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₃ P₃ ZKHQWZAMYRWXGA-KQYNXXCUSA-N		Interactions Focus chain I [auth A] Focus chain N [auth D] Focus chain S [auth F] Focus chain Y [auth H] Interactions & Density Focus chain I [auth A] Focus chain N [auth D] Focus chain S [auth F] Focus chain Y [auth H]
A1CXI( Subject of Investigation/LOI) Query on A1CXI Download:Ideal Coordinates CCD File SDF format, chain M [auth A] SDF format, chain R [auth D] SDF format, chain W [auth F] SDF format, chain X [auth H] MOL2 format, chain M [auth A] MOL2 format, chain R [auth D] MOL2 format, chain W [auth F] MOL2 format, chain X [auth H] mmCIF format, chain M [auth A] mmCIF format, chain R [auth D] mmCIF format, chain W [auth F] mmCIF format, chain X [auth H]	M [auth A], R [auth D], W [auth F], X [auth H]	(1P)-2,2',3,5',6-pentachloro-1,1'-biphenyl C₁₂ H₅ Cl₅ GXNNLIMMEXHBKV-UHFFFAOYSA-N		Interactions Focus chain M [auth A] Focus chain R [auth D] Focus chain W [auth F] Focus chain X [auth H] Interactions & Density Focus chain M [auth A] Focus chain R [auth D] Focus chain W [auth F] Focus chain X [auth H]
CFF Query on CFF Download:Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain O [auth D] SDF format, chain T [auth F] SDF format, chain Z [auth H] MOL2 format, chain J [auth A] MOL2 format, chain O [auth D] MOL2 format, chain T [auth F] MOL2 format, chain Z [auth H] mmCIF format, chain J [auth A] mmCIF format, chain O [auth D] mmCIF format, chain T [auth F] mmCIF format, chain Z [auth H]	J [auth A], O [auth D], T [auth F], Z [auth H]	CAFFEINE C₈ H₁₀ N₄ O₂ RYYVLZVUVIJVGH-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain O [auth D] Focus chain T [auth F] Focus chain Z [auth H] Interactions & Density Focus chain J [auth A] Focus chain O [auth D] Focus chain T [auth F] Focus chain Z [auth H]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain BA [auth H] SDF format, chain L [auth A] SDF format, chain Q [auth D] SDF format, chain V [auth F] MOL2 format, chain BA [auth H] MOL2 format, chain L [auth A] MOL2 format, chain Q [auth D] MOL2 format, chain V [auth F] mmCIF format, chain BA [auth H] mmCIF format, chain L [auth A] mmCIF format, chain Q [auth D] mmCIF format, chain V [auth F]	BA [auth H], L [auth A], Q [auth D], V [auth F]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain BA [auth H] Focus chain L [auth A] Focus chain Q [auth D] Focus chain V [auth F] Interactions & Density Focus chain BA [auth H] Focus chain L [auth A] Focus chain Q [auth D] Focus chain V [auth F]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain AA [auth H] SDF format, chain K [auth A] SDF format, chain P [auth D] SDF format, chain U [auth F] MOL2 format, chain AA [auth H] MOL2 format, chain K [auth A] MOL2 format, chain P [auth D] MOL2 format, chain U [auth F] mmCIF format, chain AA [auth H] mmCIF format, chain K [auth A] mmCIF format, chain P [auth D] mmCIF format, chain U [auth F]	AA [auth H], K [auth A], P [auth D], U [auth F]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain AA [auth H] Focus chain K [auth A] Focus chain P [auth D] Focus chain U [auth F] Interactions & Density Focus chain AA [auth H] Focus chain K [auth A] Focus chain P [auth D] Focus chain U [auth F]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.87 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.21.2_5419:
RECONSTRUCTION	cryoSPARC	4.6.2

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2026-10-07

Deposition Author(s):

Van Petegem, F.

Funding Organization	Location	Grant Number
Canadian Institutes of Health Research (CIHR)	Canada	PJT-159601
Chinese Scholarship Council	China	202306250027

Revision History (Full details and data files)

Version 1.0: 2026-10-07
Type: Initial release