6JIU

Structure of RyR2 (F/A/C/L-Ca2+/Ca2+CaM dataset)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.20 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, D, G, J4968Sus scrofaMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Peptidyl-prolyl cis-trans isomerase FKBP1BB, E, H, K108Homo sapiensMutation(s): 0 
Gene Names: FKBP1B, FKBP12.6, FKBP1L, FKBP9, OTK4
EC: 5.2.1.8
UniProt & NIH Common Fund Data Resources
Find proteins for P68106 (Homo sapiens)
Explore P68106 
Go to UniProtKB:  P68106
PHAROS:  P68106
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP68106
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Calmodulin-1C, F, I, L149Homo sapiensMutation(s): 0 
Gene Names: CALM1, CALM, CAM, CAM1
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
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP
Download Ideal Coordinates CCD File 
AA [auth G],
GA [auth J],
O [auth A],
U [auth D]		ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N		 Ligand Interaction
CFF
Query on CFF
Download Ideal Coordinates CCD File 
BA [auth G],
HA [auth J],
P [auth A],
V [auth D]		CAFFEINE
C8 H10 N4 O2
RYYVLZVUVIJVGH-UHFFFAOYSA-N		 Ligand Interaction
ZN
Query on ZN
Download Ideal Coordinates CCD File 
EA [auth J],
M [auth A],
S [auth D],
Y [auth G]		ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N		 Ligand Interaction
CA
Query on CA
Download Ideal Coordinates CCD File 
CA [auth I],
DA [auth I],
FA [auth J],
IA [auth L],
JA [auth L],
CA [auth I],
DA [auth I],
FA [auth J],
IA [auth L],
JA [auth L],
N [auth A],
Q [auth C],
R [auth C],
T [auth D],
W [auth F],
X [auth F],
Z [auth G]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



View more in-depth experimental data

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