Biological Assembly 1  

 3D View: Structure | Ligand Interaction

Global Symmetry: Cyclic - C4  (3D View)
Global Stoichiometry: Hetero 12-mer - A4BC 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 2378.10 kDa 
• Atom Count: 115288 
• Residue Count: 15056 
• Unique protein chains: 3

6JIY

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

• DOI: 10.2210/pdb6JIY/pdb
• EMDataResource: EMD-9837

• Classification: MEMBRANE PROTEIN
• Organism(s): Sus scrofa, Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2019-02-24 Released: 2019-07-17 
• Deposition Author(s): Gong, D.S., Chi, X.M., Zhou, G.W., Huang, G.X.Y., Lei, J.L., Yan, N.

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.90 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

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

• PubMed: 31278385 
• DOI: 10.1038/s41586-019-1377-y
• Structures With Same Primary Citation


• 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.

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Organizational Affiliation: 

Department of Molecular Biology, Princeton University, Princeton, NJ, USA. [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
RyR2	A, D, G, J	4968	Sus scrofa	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
Peptidyl-prolyl cis-trans isomerase FKBP1B	B, E, H, K	108	Homo sapiens	Mutation(s): 0  Gene Names: FKBP1B, FKBP12.6, FKBP1L, FKBP9, OTK4 EC: 5.2.1.8
Find proteins for P68106 (Homo sapiens) Go to UniProtKB:  P68106
NIH Common Fund Data Resources
PHAROS  P68106 GTEx  ENSG00000119782

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details
Calmodulin-1	C, F, I, L	149	Homo sapiens	Mutation(s): 0  Gene Names: CALM1, CALM, CAM, CAM1
Find proteins for P0DP23 (Homo sapiens) Go to UniProtKB:  P0DP23
NIH Common Fund Data Resources
PHAROS  P0DP23 GTEx  ENSG00000198668

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ATP	A, D, G, J	ADENOSINE-5'-TRIPHOSPHATE C10 H16 N5 O13 P3 ZKHQWZAMYRWXGA-KQYNXXCUSA-N
CFF	A, D, G, J	CAFFEINE C8 H10 N4 O2 RYYVLZVUVIJVGH-UHFFFAOYSA-N
ZN	A, D, G, J	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CA	A, C, D, F, G, I, J, L	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 

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2019-02-24 
• Released Date: 2019-07-17 
Deposition Author(s): Gong, D.S., Chi, X.M., Zhou, G.W., Huang, G.X.Y., Lei, J.L., Yan, N.

Revision History 

• 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