9CGP

RyR1 disease mutant Y523S with FKBP12.6, nanodisc and inhibitor dantrolene in the absence of calcium with refined P1 domain

• PDB DOI: https://doi.org/10.2210/pdb9CGP/pdb
• EM Map EMD-45584: EMDB EMDataResource

• Classification: MEMBRANE PROTEIN
• Organism(s): Oryctolagus cuniculus, Homo sapiens
• Expression System: Homo sapiens, Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): Yes 


• Deposited: 2024-06-30 Released: 2024-12-11 
• Deposition Author(s): Iyer, K.A., Samso, M.
• Funding Organization(s): National Institutes of Health/National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIH/NIAMS), American Heart Association, Other private, National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.34 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental

Literature

Manuscript in preparation

Iyer, K.A., Kobayashi, T., Murayama, T., Samso, M.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: electron microscopy

Macromolecule Content

• Total Structure Weight: 2,313.55 kDa 
• Atom Count: 132,860 
• Modelled Residue Count: 17,460 
• Deposited Residue Count: 20,576 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ryanodine receptor 1	A, B, C, D	5,037	Oryctolagus cuniculus	Mutation(s): 1  Gene Names: RYR1
UniProt
Find proteins for P11716 (Oryctolagus cuniculus) Explore P11716  Go to UniProtKB:  P11716

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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ATP (Subject of Investigation/LOI)	J [auth A], M [auth B], P [auth C], S [auth D]	ADENOSINE-5'-TRIPHOSPHATE C10 H16 N5 O13 P3 ZKHQWZAMYRWXGA-KQYNXXCUSA-N
U1C (Subject of Investigation/LOI)	K [auth A], N [auth B], Q [auth C], T [auth D]	Dantrolene C14 H10 N4 O5 OZOMQRBLCMDCEG-CHHVJCJISA-N
ZN (Subject of Investigation/LOI)	I [auth A], L [auth B], O [auth C], R [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.34 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC	3.3.1
MODEL REFINEMENT	PHENIX	20

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-12-11 
Deposition Author(s): Iyer, K.A., Samso, M.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIH/NIAMS)	United States	R01 AR068431
American Heart Association	United States	19POST34430178
Other private		MDA 352845
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	U24 GM116789
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	U24 GM116790

Revision History  

• Version 1.0: 2024-12-11
  Type: Initial release