4JKQ | pdb_00004jkq

Crystal structure of the N-terminal region of the human ryanodine receptor 2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.39 Å
  • R-Value Free: 
    0.261 (Depositor), 0.258 (DCC) 
  • R-Value Work: 
    0.224 (Depositor), 0.223 (DCC) 
  • R-Value Observed: 
    0.226 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.3 of the entry. See complete history

Literature

Structural insights into the human RyR2 N-terminal region involved in cardiac arrhythmias.

Borko, L.Bauerova-Hlinkova, V.Hostinova, E.Gasperik, J.Beck, K.Lai, F.A.Zahradnikova, A.Sevcik, J.

(2014) Acta Crystallogr D Biol Crystallogr 70: 2897-2912

  • DOI: https://doi.org/10.1107/S1399004714020343
  • Primary Citation Related Structures: 
    4JKQ

  • PubMed Abstract: 

    Human ryanodine receptor 2 (hRyR2) mediates calcium release from the sarcoplasmic reticulum, enabling cardiomyocyte contraction. The N-terminal region of hRyR2 (amino acids 1-606) is the target of >30 arrhythmogenic mutations and contains a binding site for phosphoprotein phosphatase 1. Here, the solution and crystal structures determined under near-physiological conditions, as well as a homology model of the hRyR2 N-terminal region, are presented. The N-terminus is held together by a unique network of interactions among its three domains, A, B and C, in which the central helix (amino acids 410-437) plays a prominent stabilizing role. Importantly, the anion-binding site reported for the mouse RyR2 N-terminal region is notably absent from the human RyR2. The structure concurs with the differential stability of arrhythmogenic mutations in the central helix (R420W, I419F and I419F/R420W) which are owing to disparities in the propensity of mutated residues to form energetically favourable or unfavourable contacts. In solution, the N-terminus adopts a globular shape with a prominent tail that is likely to involve residues 545-606, which are unresolved in the crystal structure. Docking the N-terminal domains into cryo-electron microscopy maps of the closed and open RyR1 conformations reveals C(α) atom movements of up to 8 Å upon channel gating, and predicts the location of the leucine-isoleucine zipper segment and the interaction site for spinophilin and phosphoprotein phosphatase 1 on the RyR surface.


  • Organizational Affiliation
    • Department of Biochemistry and Structural Biology, Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská cesta 21, 845 51 Bratislava, Slovakia.

Macromolecule Content 

  • Total Structure Weight: 67.92 kDa 
  • Atom Count: 4,013 
  • Modeled Residue Count: 499 
  • Deposited Residue Count: 606 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Ryanodine receptor 2606Homo sapiensMutation(s): 0 
Gene Names: RYR2
UniProt & NIH Common Fund Data Resources
Find proteins for Q92736 (Homo sapiens)
Explore Q92736 
Go to UniProtKB:  Q92736
PHAROS:  Q92736
GTEx:  ENSG00000198626 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ92736
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.39 Å
  • R-Value Free:  0.261 (Depositor), 0.258 (DCC) 
  • R-Value Work:  0.224 (Depositor), 0.223 (DCC) 
  • R-Value Observed: 0.226 (Depositor) 
Space Group: P 42 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 75.45α = 90
b = 75.45β = 90
c = 248.84γ = 90
Software Package:
Software NamePurpose
MAR345dtbdata collection
MOLREPphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-04-02
    Type: Initial release
  • Version 1.1: 2014-11-12
    Changes: Database references
  • Version 1.2: 2014-12-24
    Changes: Database references
  • Version 1.3: 2023-09-20
    Changes: Data collection, Database references, Refinement description