Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content

• Total Structure Weight: 2,425.39 kDa 
• Atom Count: 143,048 
• Modelled Residue Count: 17,940 
• Deposited Residue Count: 21,548 
• Unique protein chains: 2

 8SET

Cryo-EM Structure of RyR1 + cAMP

• PDB DOI:  https://doi.org/10.2210/pdb8SET/pdb
• EM Map EMD-40428: EMDB EMDataResource

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


• Deposited: 2023-04-10 Released: 2023-05-24 
• Deposition Author(s): Cholak, S., Saville, J.W., Zhu, X., Berezuk, A.M., Tuttle, K.S., Haji-Ghassemi, O., Van Petegem, F., Subramaniam, S.
• Funding Organization(s): Canada Excellence Research Chair Award, Canadian Institutes of Health Research (CIHR)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.42 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Allosteric modulation of ryanodine receptor RyR1 by nucleotide derivatives.

Cholak, S., Saville, J.W., Zhu, X., Berezuk, A.M., Tuttle, K.S., Haji-Ghassemi, O., Alvarado, F.J., Van Petegem, F., Subramaniam, S.

(2023) Structure 

• PubMed: 37192614 
• DOI: https://doi.org/10.1016/j.str.2023.04.009
• Primary Citation of Related Structures:  
  8SEN, 8SEO, 8SEP, 8SEQ, 8SER, 8SES, 8SET, 8SEU, 8SEV, 8SEW, 8SEX, 8SEY, 8SEZ, 8SF0


• PubMed Abstract: 
  

The coordinated release of Ca ²⁺ from the sarcoplasmic reticulum (SR) is critical for excitation-contraction coupling. This release is facilitated by ryanodine receptors (RyRs) that are embedded in the SR membrane. In skeletal muscle, activity of RyR1 is regulated by metabolites such as ATP, which upon binding increase channel open probability (P _o ). To obtain structural insights into the mechanism of RyR1 priming by ATP, we determined several cryo-EM structures of RyR1 bound individually to ATP-γ-S, ADP, AMP, adenosine, adenine, and cAMP. We demonstrate that adenine and adenosine bind RyR1, but AMP is the smallest ATP derivative capable of inducing long-range (>170 Å) structural rearrangements associated with channel activation, establishing a structural basis for key binding site interactions that are the threshold for triggering quaternary structural changes. Our finding that cAMP also induces these structural changes and results in increased channel opening suggests its potential role as an endogenous modulator of RyR1 conductance.

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Organizational Affiliation: 

Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC V6T 1Z3, Canada. Electronic address: [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ryanodine receptor 1	A, B, C, D	5,037	Oryctolagus cuniculus	Mutation(s): 0  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
Glutathione S-transferase class-mu 26 kDa isozyme,Peptidyl-prolyl cis-trans isomerase FKBP1B	E, F, G, H	350	Homo sapiens	Mutation(s): 0  Gene Names: FKBP1B, FKBP12.6, FKBP1L, FKBP9, OTK4 EC: 2.5.1.18 (PDB Primary Data), 5.2.1.8 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for P08515 (Schistosoma japonicum) Explore P08515  Go to UniProtKB:  P08515
Find proteins for P68106 (Homo sapiens) Explore P68106  Go to UniProtKB:  P68106
PHAROS:  P68106
UniProt Groups	P68106P08515

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CMP (Subject of Investigation/LOI)	I [auth A], K [auth B], M [auth C], O [auth D]	ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE C10 H12 N5 O6 P IVOMOUWHDPKRLL-KQYNXXCUSA-N
ZN	J [auth A], L [auth B], N [auth C], P [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.42 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-05-24 
Deposition Author(s): Cholak, S., Saville, J.W., Zhu, X., Berezuk, A.M., Tuttle, K.S., Haji-Ghassemi, O., Van Petegem, F., Subramaniam, S.

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Funding Organization	Location	Grant Number
Canada Excellence Research Chair Award	Canada	--
Canadian Institutes of Health Research (CIHR)	Canada	--

Revision History  

• Version 1.0: 2023-05-24
  Type: Initial release
  
• Version 1.1: 2023-05-31
  Changes: Database references