5GKZ

Structure of RyR1 in a closed state (C3 conformer)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

The Central domain of RyR1 is the transducer for long-range allosteric gating of channel opening

Bai, X.C.Yan, Z.Wu, J.P.Li, Z.Q.Yan, N.

(2016) Cell Res. 26: 995-1006

  • DOI: 10.1038/cr.2016.89
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The ryanodine receptors (RyRs) are intracellular calcium channels responsible for rapid release of Ca(2+) from the sarcoplasmic/endoplasmic reticulum (SR/ER) to the cytoplasm, which is essential for the excitation-contraction (E-C) coupling of cardia ...

    The ryanodine receptors (RyRs) are intracellular calcium channels responsible for rapid release of Ca(2+) from the sarcoplasmic/endoplasmic reticulum (SR/ER) to the cytoplasm, which is essential for the excitation-contraction (E-C) coupling of cardiac and skeletal muscles. The near-atomic resolution structure of closed RyR1 revealed the molecular details of this colossal channel, while the long-range allosteric gating mechanism awaits elucidation. Here, we report the cryo-EM structures of rabbit RyR1 in three closed conformations at about 4 Å resolution and an open state at 5.7 Å. Comparison of the closed RyR1 structures shows a breathing motion of the cytoplasmic platform, while the channel domain and its contiguous Central domain remain nearly unchanged. Comparison of the open and closed structures shows a dilation of the S6 tetrahelical bundle at the cytoplasmic gate that leads to channel opening. During the pore opening, the cytoplasmic "O-ring" motif of the channel domain and the U-motif of the Central domain exhibit coupled motion, while the Central domain undergoes domain-wise displacement. These structural analyses provide important insight into the E-C coupling in skeletal muscles and identify the Central domain as the transducer that couples the conformational changes of the cytoplasmic platform to the gating of the central pore.


    Organizational Affiliation

    State Key Laboratory of Membrane Biology, Tsinghua University, Beijing 100084, China.,MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK.,Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences and School of Medicine, Tsinghua University, Beijing 100084, China.,Beijing Advanced Innovation Center for Structural Biology, Tsinghua University, Beijing 100084, China.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ryanodine receptor 1
A, C, E, G
5037Oryctolagus cuniculusMutation(s): 0 
Gene Names: RYR1
Find proteins for P11716 (Oryctolagus cuniculus)
Go to Gene View: RYR1
Go to UniProtKB:  P11716
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Peptidyl-prolyl cis-trans isomerase FKBP1A
B, D, F, H
108Oryctolagus cuniculusMutation(s): 0 
Gene Names: FKBP1A (FKBP1, FKBP12)
EC: 5.2.1.8
Find proteins for P62943 (Oryctolagus cuniculus)
Go to Gene View: FKBP1A
Go to UniProtKB:  P62943
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, C, E, G
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
the Ministry of Science and Technology of ChinaChina2015CB9101012014, ZX09507003006
National Natural Science Foundation of ChinaChinaproject 31321062 and 81590761

Revision History 

  • Version 1.0: 2016-08-24
    Type: Initial release
  • Version 1.1: 2016-09-14
    Type: Database references
  • Version 1.2: 2016-09-21
    Type: Other
  • Version 1.3: 2019-10-16
    Type: Data collection, Other