6JIY

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


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.90 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: https://doi.org/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. 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

    Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
RyR2
A, D, G, J
4,968Sus scrofaMutation(s): 0 
Entity Groups  
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Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Peptidyl-prolyl cis-trans isomerase FKBP1B
B, E, H, K
108Homo sapiensMutation(s): 0 
Gene Names: FKBP1BFKBP12.6FKBP1LFKBP9OTK4
EC: 5.2.1.8
UniProt & NIH Common Fund Data Resources
Find proteins for P68106 (Homo sapiens)
Explore P68106 
Go to UniProtKB:  P68106
GTEx:  ENSG00000119782 
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UniProt GroupP68106
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Calmodulin-1
C, F, I, L
149Homo sapiensMutation(s): 0 
Gene Names: CALM1CALMCAMCAM1
UniProt & NIH Common Fund Data Resources
Find proteins for P0DP23 (Homo sapiens)
Explore P0DP23 
Go to UniProtKB:  P0DP23
GTEx:  ENSG00000198668 
Entity Groups  
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UniProt GroupP0DP23
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP

Download Ideal Coordinates CCD File 
EA [auth G],
MA [auth J],
O [auth A],
W [auth D]
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
CFF
Query on CFF

Download Ideal Coordinates CCD File 
FA [auth G],
NA [auth J],
P [auth A],
X [auth D]
CAFFEINE
C8 H10 N4 O2
RYYVLZVUVIJVGH-UHFFFAOYSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
CA [auth G],
KA [auth J],
M [auth A],
U [auth D]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
AA [auth F]
BA [auth F]
DA [auth G]
GA [auth I]
HA [auth I]
AA [auth F],
BA [auth F],
DA [auth G],
GA [auth I],
HA [auth I],
IA [auth I],
JA [auth I],
LA [auth J],
N [auth A],
OA [auth L],
PA [auth L],
Q [auth C],
QA [auth L],
R [auth C],
RA [auth L],
S [auth C],
T [auth C],
V [auth D],
Y [auth F],
Z [auth F]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION2.0

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