7UA4

Structure of PKA phosphorylated human RyR2-R2474S in the open state in the presence of Calmodulin


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.93 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


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Literature

Structural analyses of human ryanodine receptor type 2 channels reveal the mechanisms for sudden cardiac death and treatment.

Miotto, M.C.Weninger, G.Dridi, H.Yuan, Q.Liu, Y.Wronska, A.Melville, Z.Sittenfeld, L.Reiken, S.Marks, A.R.

(2022) Sci Adv 8: eabo1272-eabo1272

  • DOI: 10.1126/sciadv.abo1272
  • Primary Citation of Related Structures:  
    7U9Q, 7U9R, 7U9T, 7U9X, 7U9Z, 7UA1, 7UA3, 7UA4, 7UA5, 7UA9

  • PubMed Abstract: 
  • Ryanodine receptor type 2 (RyR2) mutations have been linked to an inherited form of exercise-induced sudden cardiac death called catecholaminergic polymorphic ventricular tachycardia (CPVT). CPVT results from stress-induced sarcoplasmic reticular Ca 2+ leak via the mutant RyR2 channels during diastole ...

    Ryanodine receptor type 2 (RyR2) mutations have been linked to an inherited form of exercise-induced sudden cardiac death called catecholaminergic polymorphic ventricular tachycardia (CPVT). CPVT results from stress-induced sarcoplasmic reticular Ca 2+ leak via the mutant RyR2 channels during diastole. We present atomic models of human wild-type (WT) RyR2 and the CPVT mutant RyR2-R2474S determined by cryo-electron microscopy with overall resolutions in the range of 2.6 to 3.6 Å, and reaching local resolutions of 2.25 Å, unprecedented for RyR2 channels. Under nonactivating conditions, the RyR2-R2474S channel is in a "primed" state between the closed and open states of WT RyR2, rendering it more sensitive to activation that results in stress-induced Ca 2+ leak. The Rycal drug ARM210 binds to RyR2-R2474S, reverting the primed state toward the closed state. Together, these studies provide a mechanism for CPVT and for the therapeutic actions of ARM210.


    Organizational Affiliation

    Clyde and Helen Wu Center for Molecular Cardiology, Columbia University, New York, NY, USA.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Ryanodine receptor 2A,
J [auth B],
K [auth C],
L [auth D]
4967Homo sapiensMutation(s): 1 
Gene Names: RYR2
UniProt & NIH Common Fund Data Resources
Find proteins for Q92736 (Homo sapiens)
Explore Q92736 
Go to UniProtKB:  Q92736
PHAROS:  Q92736
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ92736
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Peptidyl-prolyl cis-trans isomerase FKBP1BB [auth E],
C [auth F],
D [auth G],
E [auth H]
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
PHAROS:  P68106
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UniProt GroupP68106
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Calmodulin-1F [auth I],
G [auth J],
H [auth K],
I [auth L]
149Homo sapiensMutation(s): 0 
Gene Names: CALM1CALMCAMCAM1
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Find proteins for P0DP23 (Homo sapiens)
Explore P0DP23 
Go to UniProtKB:  P0DP23
PHAROS:  P0DP23
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UniProt GroupP0DP23
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ATP (Subject of Investigation/LOI)
Query on ATP

Download Ideal Coordinates CCD File 
AA [auth C],
CA [auth D],
FA [auth D],
N [auth A],
Q [auth A],
AA [auth C],
CA [auth D],
FA [auth D],
N [auth A],
Q [auth A],
S [auth B],
V [auth B],
X [auth C]
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
 Ligand Interaction
XAN (Subject of Investigation/LOI)
Query on XAN

Download Ideal Coordinates CCD File 
EA [auth D],
P [auth A],
U [auth B],
Z [auth C]
XANTHINE
C5 H4 N4 O2
LRFVTYWOQMYALW-UHFFFAOYSA-N
 Ligand Interaction
ZN (Subject of Investigation/LOI)
Query on ZN

Download Ideal Coordinates CCD File 
BA [auth D],
M [auth A],
R [auth B],
W [auth C]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
CA (Subject of Investigation/LOI)
Query on CA

Download Ideal Coordinates CCD File 
DA [auth D],
O [auth A],
T [auth B],
Y [auth C]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.93 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)United StatesR01HL145473

Revision History  (Full details and data files)

  • Version 1.0: 2022-08-03
    Type: Initial release