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, 6JI8, 6JII, 6JIU, 6JIY, 6JRR, 6JRS, 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)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
RyR2A, C, E, G4,968Sus scrofaMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Protein Feature View
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  • Reference Sequence
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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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0DP23
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],
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