7K0S

Cryo-EM structure of rabbit RyR1 in the presence of Mg2+ and AMP-PCP in nanodisc

  • Classification: TRANSPORT PROTEIN
  • Organism(s): Oryctolagus cuniculus
  • Mutation(s): No 

  • Deposited: 2020-09-05 Released: 2021-09-22 
  • Deposition Author(s): Nayak, A.R., Samso, M.
  • Funding Organization(s): National Institutes of Health/National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIH/NIAMS), National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI), Other private, National Institutes of Health/National Cancer Institute (NIH/NCI), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 2.1 of the entry. See complete history. 


Literature

Interplay between Mg2+ and Ca2+ at multiple sites of the ryanodine receptor

Nayak, A.R., Rangubpit, W., Will, A.H., Hu , Y., Castro-Hartmann, P., Lobo, J.J., Dryden, K., Lamb, G.D., Sompornpisut, P., Samso, M.

(2024) Biorxiv 


Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
RyR1A,
B,
C [auth D],
D [auth C]		5,037Oryctolagus cuniculusMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ACP
Query on ACP
Download Ideal Coordinates CCD File 
E [auth A],
H [auth B],
L [auth D],
O [auth C]		PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER
C11 H18 N5 O12 P3
UFZTZBNSLXELAL-IOSLPCCCSA-N
ZN
Query on ZN
Download Ideal Coordinates CCD File 
F [auth A],
I [auth B],
M [auth D],
P [auth C]		ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG (Subject of Investigation/LOI)
Query on MG
Download Ideal Coordinates CCD File 
G [auth A],
J [auth B],
K [auth B],
N [auth D],
Q [auth C]		MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIXdev-3958-000
RECONSTRUCTIONRELION1.4

Structure Validation

View Full Validation Report



View more in-depth experimental data
Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIH/NIAMS)United StatesR01 AR068431
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)United StatesR01 HL133182
Other privateUnited StatesMDA 352845
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesHSSN261200800001E
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesU24 GM116789
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesU24 GM116790

Revision History  (Full details and data files)

  • Version 1.0: 2021-09-22
    Type: Initial release
  • Version 2.0: 2022-03-09
    Type: Coordinate replacement
    Reason: Polymer backbone linkage
    Changes: Advisory, Atomic model, Author supporting evidence, Data collection, Database references, Derived calculations, Experimental preparation, Polymer sequence, Source and taxonomy, Structure summary
  • Version 2.1: 2024-02-28
    Changes: Data collection, Database references