3J8H

Structure of the rabbit ryanodine receptor RyR1 in complex with FKBP12 at 3.8 Angstrom resolution


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.8 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Structure of the rabbit ryanodine receptor RyR1 at near-atomic resolution.

Yan, Z.Bai, X.C.Yan, C.Wu, J.Li, Z.Xie, T.Peng, W.Yin, C.C.Li, X.Scheres, S.H.Shi, Y.Yan, N.

(2015) Nature 517: 50-55

  • DOI: 10.1038/nature14063

  • PubMed Abstract: 
  • The ryanodine receptors (RyRs) are high-conductance intracellular Ca(2+) channels that play a pivotal role in the excitation-contraction coupling of skeletal and cardiac muscles. RyRs are the largest known ion channels, with a homotetrameric organiza ...

    The ryanodine receptors (RyRs) are high-conductance intracellular Ca(2+) channels that play a pivotal role in the excitation-contraction coupling of skeletal and cardiac muscles. RyRs are the largest known ion channels, with a homotetrameric organization and approximately 5,000 residues in each protomer. Here we report the structure of the rabbit RyR1 in complex with its modulator FKBP12 at an overall resolution of 3.8 Å, determined by single-particle electron cryomicroscopy. Three previously uncharacterized domains, named central, handle and helical domains, display the armadillo repeat fold. These domains, together with the amino-terminal domain, constitute a network of superhelical scaffold for binding and propagation of conformational changes. The channel domain exhibits the voltage-gated ion channel superfamily fold with distinct features. A negative-charge-enriched hairpin loop connecting S5 and the pore helix is positioned above the entrance to the selectivity-filter vestibule. The four elongated S6 segments form a right-handed helical bundle that closes the pore at the cytoplasmic border of the membrane. Allosteric regulation of the pore by the cytoplasmic domains is mediated through extensive interactions between the central domains and the channel domain. These structural features explain high ion conductance by RyRs and the long-range allosteric regulation of channel activities.


    Organizational Affiliation

    State Key Laboratory of Bio-membrane and Membrane Biotechnology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences and School of Medicine, Tsinghua University, Beijing 100084, China.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ryanodine receptor 1
A, C, E, G
4599Oryctolagus cuniculusMutation(s): 0 
Gene Names: RYR1
Membrane protein
mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Channels: Calcium Ion-Selective
Protein: 
RyR1 ryanodine receptor, closed state in complex with FKBP12. Cryo-EM structure
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
107Oryctolagus cuniculusMutation(s): 0 
Gene Names: FKBP1A (FKBP1, FKBP12)
EC: 5.2.1.8
Membrane protein
mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Channels: Calcium Ion-Selective
Protein: 
RyR1 ryanodine receptor, closed state in complex with FKBP12. Cryo-EM structure
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
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
UNK
Query on UNK
A, C, E, G
L-PEPTIDE LINKINGC4 H9 N O2

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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.8 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
Software Package:
Software NamePurpose
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-12-10
    Type: Initial release
  • Version 1.1: 2014-12-17
    Type: Advisory
  • Version 1.2: 2015-01-21
    Type: Structure summary
  • Version 1.3: 2015-02-25
    Type: Database references
  • Version 1.4: 2018-07-18
    Type: Data collection