6JV2

Structure of RyR2 (P/L-Ca2+/Ca2+-CaM dataset)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.40 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

Modulation of cardiac ryanodine receptor 2 by calmodulin.

Gong, D.Chi, X.Wei, J.Zhou, G.Huang, G.Zhang, L.Wang, R.Lei, J.Chen, S.R.W.Yan, N.

(2019) Nature 572: 347-351

  • DOI: 10.1038/s41586-019-1377-y
  • Primary Citation of Related Structures:  
    6JI0, 6JII, 6JI8, 6JIU, 6JIY, 6JRS, 6JRR, 6JV2

  • PubMed Abstract: 
  • The high-conductance intracellular calcium (Ca 2+ ) channel RyR2 is essential for the coupling of excitation and contraction in cardiac muscle. Among various modulators, calmodulin (CaM) regulates RyR2 in a Ca 2+ -dependent manner. Here we reveal the regulatory mechanism by which porcine RyR2 is modulated by human CaM through the structural determination of RyR2 under eight conditions ...

    The high-conductance intracellular calcium (Ca 2+ ) channel RyR2 is essential for the coupling of excitation and contraction in cardiac muscle. Among various modulators, calmodulin (CaM) regulates RyR2 in a Ca 2+ -dependent manner. Here we reveal the regulatory mechanism by which porcine RyR2 is modulated by human CaM through the structural determination of RyR2 under eight conditions. Apo-CaM and Ca 2+ -CaM bind to distinct but overlapping sites in an elongated cleft formed by the handle, helical and central domains. The shift in CaM-binding sites on RyR2 is controlled by Ca 2+ binding to CaM, rather than to RyR2. Ca 2+ -CaM induces rotations and intradomain shifts of individual central domains, resulting in pore closure of the PCB95 and Ca 2+ -activated channel. By contrast, the pore of the ATP, caffeine and Ca 2+ -activated channel remains open in the presence of Ca 2+ -CaM, which suggests that Ca 2+ -CaM is one of the many competing modulators of RyR2 gating.


    Organizational Affiliation

    Department of Molecular Biology, Princeton University, Princeton, NJ, USA. nyan@princeton.edu.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
RyR2A, C, E, G4968Sus scrofaMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Calmodulin-1B, D, F, H149Homo sapiensMutation(s): 0 
Gene Names: CALM1CALMCAMCAM1
UniProt & NIH Common Fund Data Resources
Find proteins for P0DP23 (Homo sapiens)
Explore P0DP23 
Go to UniProtKB:  P0DP23
PHAROS:  P0DP23
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
AA [auth G], I [auth A], O [auth C], U [auth E]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download Ideal Coordinates CCD File 
BA [auth G] , CA [auth H] , DA [auth H] , EA [auth H] , FA [auth H] , J [auth A] , K [auth B] , L [auth B] , 
BA [auth G],  CA [auth H],  DA [auth H],  EA [auth H],  FA [auth H],  J [auth A],  K [auth B],  L [auth B],  M [auth B],  N [auth B],  P [auth C],  Q [auth D],  R [auth D],  S [auth D],  T [auth D],  V [auth E],  W [auth F],  X [auth F],  Y [auth F],  Z [auth F]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-07-17
    Type: Initial release
  • Version 1.1: 2019-08-28
    Changes: Data collection, Database references, Source and taxonomy, Structure summary
  • Version 1.2: 2019-11-06
    Changes: Data collection, Other