7TDK

Rabbit RyR1 with AMP-PCP and high Ca2+ embedded in nanodisc in closed-inactivated conformation class 3 (Dataset-A)

  • Classification: TRANSPORT PROTEIN
  • Organism(s): Oryctolagus cuniculus
  • Mutation(s): No 
  • Membrane Protein: Yes  OPM

  • Deposited: 2021-12-31 Released: 2022-03-09 
  • 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), 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: 3.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Ca 2+ -inactivation of the mammalian ryanodine receptor type 1 in a lipidic environment revealed by cryo-EM.

Nayak, A.R.Samso, M.

(2022) Elife 11

  • DOI: https://doi.org/10.7554/eLife.75568
  • Primary Citation of Related Structures:  
    7K0T, 7TDG, 7TDH, 7TDI, 7TDJ, 7TDK

  • PubMed Abstract: 

    Activation of the intracellular Ca 2+ channel ryanodine receptor (RyR) triggers a cytosolic Ca 2+ surge, while elevated cytosolic Ca 2+ inhibits the channel in a negative feedback mechanism. Cryogenic electron microscopy of rabbit RyR1 embedded in nanodiscs under partially inactivating Ca 2+ conditions revealed an open and a closed-inactivated conformation. Ca 2+ binding to the high-affinity site engages the central and C-terminal domains into a block, which pries the S6 four-helix bundle open. Further rotation of this block pushes S6 toward the central axis, closing (inactivating) the channel. Main characteristics of the Ca 2+ -inactivated conformation are downward conformation of the cytoplasmic assembly and tightly knit subunit interface contributed by a fully occupied Ca 2+ activation site, two inter-subunit resolved lipids, and two salt bridges between the EF hand domain and the S2-S3 loop validated by disease-causing mutations. The structural insight illustrates the prior Ca 2+ activation prerequisite for Ca 2+ inactivation and provides for a seamless transition from inactivated to closed conformations.


  • Organizational Affiliation

    Department of Physiology and Biophysics, Virginia Commonwealth University, Richmond, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ryanodine receptor 1,Ryanodine receptor 1,RyR1
A, B, C, D
5,037Oryctolagus cuniculusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P11716 (Oryctolagus cuniculus)
Explore P11716 
Go to UniProtKB:  P11716
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP11716
Sequence Annotations
Expand
  • 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],
I [auth B],
M [auth C],
Q [auth D]
PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER
C11 H18 N5 O12 P3
UFZTZBNSLXELAL-IOSLPCCCSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
F [auth A],
J [auth B],
N [auth C],
R [auth D]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
CA (Subject of Investigation/LOI)
Query on CA

Download Ideal Coordinates CCD File 
G [auth A]
H [auth A]
K [auth B]
L [auth B]
O [auth C]
G [auth A],
H [auth A],
K [auth B],
L [auth B],
O [auth C],
P [auth C],
S [auth D],
T [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:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3.0
MODEL REFINEMENTPHENIXdev-1.20-4444-000

Structure Validation

View Full Validation Report



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
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: 2022-03-09
    Type: Initial release
  • Version 1.1: 2022-03-16
    Changes: Database references
  • Version 1.2: 2024-10-30
    Changes: Data collection, Structure summary