7TZC

A drug and ATP binding site in type 1 ryanodine receptor

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.45 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

A drug and ATP binding site in type 1 ryanodine receptor.

Melville, Z., Dridi, H., Yuan, Q., Reiken, S., Wronska, A., Liu, Y., Clarke, O.B., Marks, A.R.

(2022) Structure 30: 1025

  • DOI: 10.1016/j.str.2022.04.010
  • Primary Citation of Related Structures:  
    7TZC

  • PubMed Abstract: 

    • The ryanodine receptor (RyR)/calcium release channel on the sarcoplasmic reticulum (SR) is required for excitation-contraction coupling in skeletal and cardiac muscle. Inherited mutations and stress-induced post-translational modifications result in an SR Ca 2+ leak that causes skeletal myopathies, heart failure, and exercise-induced sudden death ...

    The ryanodine receptor (RyR)/calcium release channel on the sarcoplasmic reticulum (SR) is required for excitation-contraction coupling in skeletal and cardiac muscle. Inherited mutations and stress-induced post-translational modifications result in an SR Ca 2+ leak that causes skeletal myopathies, heart failure, and exercise-induced sudden death. A class of therapeutics known as Rycals prevent the RyR-mediated leak, are effective in preventing disease progression and restoring function in animal models, and are in clinical trials for patients with muscle and heart disorders. Using cryogenic-electron microscopy, we present a model of RyR1 with a 2.45-Å resolution before local refinement, revealing a binding site in the RY1&2 domain (3.10 Å local resolution), where the Rycal ARM210 binds cooperatively with ATP and stabilizes the closed state of RyR1.

    Organizational Affiliation: 

    Department of Physiology and Cellular Biophysics, Columbia University, New York, NY, USA; Clyde & Helen Wu Center for Molecular Cardiology, Columbia University, New York, NY, USA. Electronic address: arm42@cumc.columbia.edu.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Calmodulin-1E [auth C],
C [auth D],
D [auth E],
A [auth K]		150Homo 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
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Peptidyl-prolyl cis-trans isomerase FKBP1AB [auth F],
J [auth H],
K [auth J],
L [auth O]		107Oryctolagus cuniculusMutation(s): 0 
Gene Names: FKBP1A, FKBP1, FKBP12
EC: 5.2.1.8
Membrane Entity: Yes 
UniProt
Find proteins for P62943 (Oryctolagus cuniculus)
Explore P62943 
Go to UniProtKB:  P62943
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UniProt GroupP62943
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Ryanodine receptor 1F [auth A],
G [auth B],
H [auth G],
I		5,037Oryctolagus cuniculusMutation(s): 0 
Gene Names: RYR1
Membrane Entity: Yes 
UniProt
Find proteins for P11716 (Oryctolagus cuniculus)
Explore P11716 
Go to UniProtKB:  P11716
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP11716
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
L9R
Query on L9R
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AB [auth I],
HB [auth I],
IA [auth A],
JA [auth A],
QA [auth B],
AB [auth I],
HB [auth I],
IA [auth A],
JA [auth A],
QA [auth B],
RA [auth B],
SA [auth G],
ZA [auth G]
(2S)-3-(octadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate
C44 H86 N O8 P
ATHVAWFAEPLPPQ-FLHXZNPISA-N		 Ligand Interaction
ATP (Subject of Investigation/LOI)
Query on ATP
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BB [auth I],
CA [auth A],
FB [auth I],
GA [auth A],
KA [auth B],
BB [auth I],
CA [auth A],
FB [auth I],
GA [auth A],
KA [auth B],
OA [auth B],
TA [auth G],
XA [auth G]
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N		 Ligand Interaction
KVR
Query on KVR
Download Ideal Coordinates CCD File 
GB [auth I],
HA [auth A],
PA [auth B],
YA [auth G]		4-[(7-methoxy-2,3-dihydro-1,4-benzothiazepin-4(5H)-yl)methyl]benzoic acid
C18 H19 N O3 S
JIGDAUOKKYKRKO-UHFFFAOYSA-N		 Ligand Interaction
CFF
Query on CFF
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EB [auth I],
FA [auth A],
NA [auth B],
WA [auth G]		CAFFEINE
C8 H10 N4 O2
RYYVLZVUVIJVGH-UHFFFAOYSA-N		 Ligand Interaction
ZN
Query on ZN
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DB [auth I],
EA [auth A],
MA [auth B],
VA [auth G]		ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N		 Ligand Interaction
CA
Query on CA
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AA [auth C],
BA [auth C],
CB [auth I],
DA [auth A],
LA [auth B],
AA [auth C],
BA [auth C],
CB [auth I],
DA [auth A],
LA [auth B],
M [auth K],
N [auth K],
O [auth K],
P [auth K],
Q [auth D],
R [auth D],
S [auth D],
T [auth D],
U [auth E],
UA [auth G],
V [auth E],
W [auth E],
X [auth E],
Y [auth C],
Z [auth C]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.45 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC
MODEL REFINEMENTPHENIX

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
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)United StatesR01DK118240
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)United StatesR01HL142903
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)United StatesR01HL140934
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)United StatesR01AR070194
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)United StatesT32 HL120826

Revision History  (Full details and data files)

  • Version 1.0: 2022-05-18
    Type: Initial release
  • Version 1.1: 2022-06-29
    Changes: Database references
  • Version 1.2: 2022-07-20
    Changes: Database references