7TZC

A drug and ATP binding site in type 1 ryanodine receptor

PDB DOI: https://doi.org/10.2210/pdb7TZC/pdb
EM Map EMD-26205: EMDB EMDataResource

Classification: MEMBRANE PROTEIN
Organism(s): Homo sapiens, Oryctolagus cuniculus
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No
Membrane Protein: Yes OPM

Deposited: 2022-02-15 Released: 2022-05-18
Deposition Author(s): Melville, Z., Dridi, H., Yuan, Q., Reiken, S., Anetta, W., Liu, Y., Clarke, O.B., Marks, A.R.
Funding Organization(s): National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)

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

PubMed: 35580609 Search on PubMed
DOI: https://doi.org/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. 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.

Macromolecule Content

Total Structure Weight: 2,392.46 kDa
Atom Count: 149,472
Modelled Residue Count: 18,640
Deposited Residue Count: 21,176
Unique protein chains: 3

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Calmodulin-1	A [auth K], C [auth D], D [auth E], E [auth C]	150	Homo sapiens	Mutation(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 GTEx: ENSG00000198668
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0DP23
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptidyl-prolyl cis-trans isomerase FKBP1A	B [auth F], J [auth H], K [auth J], L [auth O]	107	Oryctolagus cuniculus	Mutation(s): 0 EC: 5.2.1.8 Membrane Entity: Yes
UniProt
Find proteins for P62943 (Oryctolagus cuniculus) Explore P62943 Go to UniProtKB: P62943
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P62943
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Ryanodine receptor 1	F [auth A], G [auth B], H [auth G], I	5,037	Oryctolagus cuniculus	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P11716 (Oryctolagus cuniculus) Explore P11716 Go to UniProtKB: P11716
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P11716
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
L9R Query on L9R Download Ideal Coordinates CCD File SDF format, chain AB [auth I] SDF format, chain HB [auth I] SDF format, chain RA [auth B] SDF format, chain IA [auth A] SDF format, chain JA [auth A] SDF format, chain QA [auth B] SDF format, chain SA [auth G] SDF format, chain ZA [auth G] MOL2 format, chain AB [auth I] MOL2 format, chain HB [auth I] MOL2 format, chain RA [auth B] MOL2 format, chain IA [auth A] MOL2 format, chain JA [auth A] MOL2 format, chain QA [auth B] MOL2 format, chain SA [auth G] MOL2 format, chain ZA [auth G]	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		Interactions Focus chain AB [auth I] Focus chain HB [auth I] Focus chain IA [auth A] Focus chain JA [auth A] Focus chain QA [auth B] Focus chain RA [auth B] Focus chain SA [auth G] Focus chain ZA [auth G] Interactions & Density Focus chain AB [auth I] Focus chain HB [auth I] Focus chain IA [auth A] Focus chain JA [auth A] Focus chain QA [auth B] Focus chain RA [auth B] Focus chain SA [auth G] Focus chain ZA [auth G]
ATP (Subject of Investigation/LOI) Query on ATP Download Ideal Coordinates CCD File SDF format, chain KA [auth B] SDF format, chain BB [auth I] SDF format, chain CA [auth A] SDF format, chain FB [auth I] SDF format, chain GA [auth A] SDF format, chain OA [auth B] SDF format, chain TA [auth G] SDF format, chain XA [auth G] MOL2 format, chain KA [auth B] MOL2 format, chain BB [auth I] MOL2 format, chain CA [auth A] MOL2 format, chain FB [auth I] MOL2 format, chain GA [auth A] MOL2 format, chain OA [auth B] MOL2 format, chain TA [auth G] MOL2 format, chain XA [auth G]	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		Interactions Focus chain BB [auth I] Focus chain CA [auth A] Focus chain FB [auth I] Focus chain GA [auth A] Focus chain KA [auth B] Focus chain OA [auth B] Focus chain TA [auth G] Focus chain XA [auth G] Interactions & Density Focus chain BB [auth I] Focus chain CA [auth A] Focus chain FB [auth I] Focus chain GA [auth A] Focus chain KA [auth B] Focus chain OA [auth B] Focus chain TA [auth G] Focus chain XA [auth G]
KVR Query on KVR Download Ideal Coordinates CCD File SDF format, chain GB [auth I] SDF format, chain HA [auth A] SDF format, chain PA [auth B] SDF format, chain YA [auth G] MOL2 format, chain GB [auth I] MOL2 format, chain HA [auth A] MOL2 format, chain PA [auth B] MOL2 format, chain YA [auth G]	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		Interactions Focus chain GB [auth I] Focus chain HA [auth A] Focus chain PA [auth B] Focus chain YA [auth G] Interactions & Density Focus chain GB [auth I] Focus chain HA [auth A] Focus chain PA [auth B] Focus chain YA [auth G]
CFF Query on CFF Download Ideal Coordinates CCD File SDF format, chain WA [auth G] SDF format, chain EB [auth I] SDF format, chain FA [auth A] SDF format, chain NA [auth B] MOL2 format, chain WA [auth G] MOL2 format, chain EB [auth I] MOL2 format, chain FA [auth A] MOL2 format, chain NA [auth B]	EB [auth I], FA [auth A], NA [auth B], WA [auth G]	CAFFEINE C₈ H₁₀ N₄ O₂ RYYVLZVUVIJVGH-UHFFFAOYSA-N		Interactions Focus chain EB [auth I] Focus chain FA [auth A] Focus chain NA [auth B] Focus chain WA [auth G] Interactions & Density Focus chain EB [auth I] Focus chain FA [auth A] Focus chain NA [auth B] Focus chain WA [auth G]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain DB [auth I] SDF format, chain MA [auth B] SDF format, chain VA [auth G] SDF format, chain EA [auth A] MOL2 format, chain DB [auth I] MOL2 format, chain MA [auth B] MOL2 format, chain VA [auth G] MOL2 format, chain EA [auth A]	DB [auth I], EA [auth A], MA [auth B], VA [auth G]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain DB [auth I] Focus chain EA [auth A] Focus chain MA [auth B] Focus chain VA [auth G] Interactions & Density Focus chain DB [auth I] Focus chain EA [auth A] Focus chain MA [auth B] Focus chain VA [auth G]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain N [auth K] SDF format, chain Q [auth D] SDF format, chain V [auth E] SDF format, chain BA [auth C] SDF format, chain CB [auth I] SDF format, chain DA [auth A] SDF format, chain LA [auth B] SDF format, chain M [auth K] SDF format, chain O [auth K] SDF format, chain P [auth K] SDF format, chain R [auth D] SDF format, chain S [auth D] SDF format, chain T [auth D] SDF format, chain U [auth E] SDF format, chain UA [auth G] SDF format, chain W [auth E] SDF format, chain X [auth E] SDF format, chain Y [auth C] SDF format, chain Z [auth C] MOL2 format, chain AA [auth C] MOL2 format, chain N [auth K] MOL2 format, chain Q [auth D] MOL2 format, chain V [auth E] MOL2 format, chain BA [auth C] MOL2 format, chain CB [auth I] MOL2 format, chain DA [auth A] MOL2 format, chain LA [auth B] MOL2 format, chain M [auth K] MOL2 format, chain O [auth K] MOL2 format, chain P [auth K] MOL2 format, chain R [auth D] MOL2 format, chain S [auth D] MOL2 format, chain T [auth D] MOL2 format, chain U [auth E] MOL2 format, chain UA [auth G] MOL2 format, chain W [auth E] MOL2 format, chain X [auth E] MOL2 format, chain Y [auth C] MOL2 format, chain Z [auth C]	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		Interactions Focus chain AA [auth C] Focus chain BA [auth C] Focus chain CB [auth I] Focus chain DA [auth A] Focus chain LA [auth B] Focus chain M [auth K] Focus chain N [auth K] Focus chain O [auth K] Focus chain P [auth K] Focus chain Q [auth D] Focus chain R [auth D] Focus chain S [auth D] Focus chain T [auth D] Focus chain U [auth E] Focus chain UA [auth G] Focus chain V [auth E] Focus chain W [auth E] Focus chain X [auth E] Focus chain Y [auth C] Focus chain Z [auth C] Interactions & Density Focus chain AA [auth C] Focus chain BA [auth C] Focus chain CB [auth I] Focus chain DA [auth A] Focus chain LA [auth B] Focus chain M [auth K] Focus chain N [auth K] Focus chain O [auth K] Focus chain P [auth K] Focus chain Q [auth D] Focus chain R [auth D] Focus chain S [auth D] Focus chain T [auth D] Focus chain U [auth E] Focus chain UA [auth G] Focus chain V [auth E] Focus chain W [auth E] Focus chain X [auth E] Focus chain Y [auth C] Focus chain Z [auth C]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.45 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC
MODEL REFINEMENT	PHENIX

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2022-05-18

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)	United States	R01HL145473
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)	United States	R01DK118240
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)	United States	R01HL142903
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)	United States	R01HL140934
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)	United States	R01AR070194
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)	United States	T32 HL120826