7VMS | pdb_00007vms

Structure of recombinant RyR2 mutant K4593A (Ca2+ dataset)

• PDB DOI: https://doi.org/10.2210/pdb7VMS/pdb
• EM Map EMD-32037: EMDB EMDataResource

• Classification: MEMBRANE PROTEIN
• Organism(s): Mus musculus, Homo sapiens
• Expression System: Homo sapiens, Escherichia coli
• Mutation(s): Yes 
• Membrane Protein: Yes  OPMmpstruc


• Deposited: 2021-10-09 Released: 2022-08-10 
• Deposition Author(s): Kobayashi, T., Tsutsumi, A., Kurebayashi, N., Kodama, M., Kikkawa, M., Murayama, T., Ogawa, H.
• Funding Organization(s): Japan Society for the Promotion of Science (JSPS), Japan Agency for Medical Research and Development (AMED)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.80 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Molecular basis for gating of cardiac ryanodine receptor explains the mechanisms for gain- and loss-of function mutations

Kobayashi, T., Tsutsumi, A., Kurebayashi, N., Saito, K., Kodama, M., Sakurai, T., Kikkawa, M., Murayama, T., Ogawa, H.

(2022) Nat Commun 13: 2821

• DOI: https://doi.org/10.1038/s41467-022-30429-x

Biological Assembly 1  

Global Symmetry: Cyclic - C4  (Explore in 3D)
Global Stoichiometry: Hetero 8-mer - A4B4 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 2,210.74 kDa 
• Atom Count: 123,552 
• Modeled Residue Count: 16,604 
• Deposited Residue Count: 20,568 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ryanodine receptor 2	A, C [auth B], E [auth C], G [auth D]	4,966	Mus musculus	Mutation(s): 1  Gene Names: Ryr2 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for E9Q401 (Mus musculus) Explore E9Q401  Go to UniProtKB:  E9Q401
IMPC:  MGI:99685

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptidyl-prolyl cis-trans isomerase FKBP1B	B [auth G], D [auth H], F [auth I], H [auth J]	176	Homo sapiens	Mutation(s): 0  Gene Names: FKBP1B 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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN (Subject of Investigation/LOI)	I [auth A], K [auth B], M [auth C], P [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CA (Subject of Investigation/LOI)	J [auth A], L [auth B], N [auth C], O [auth D]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.80 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-08-10 
Deposition Author(s): Kobayashi, T., Tsutsumi, A., Kurebayashi, N., Kodama, M., Kikkawa, M., Murayama, T., Ogawa, H.

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Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	JP16H04748
Japan Society for the Promotion of Science (JSPS)	Japan	JP19K07105
Japan Society for the Promotion of Science (JSPS)	Japan	19H03404
Japan Society for the Promotion of Science (JSPS)	Japan	JP21H02411
Japan Agency for Medical Research and Development (AMED)	Japan	JP21am0101080
Japan Agency for Medical Research and Development (AMED)	Japan	19ek0109202

Revision History  

• Version 1.0: 2022-08-10
  Type: Initial release
  
• Version 1.1: 2024-06-19
  Changes: Data collection
• Version 1.2: 2025-07-02
  Changes: Data collection, Structure summary