7UA3 | pdb_00007ua3

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

PDB DOI: https://doi.org/10.2210/pdb7UA3/pdb
EM Map EMD-26413: EMDB EMDataResource

Classification: MEMBRANE PROTEIN
Organism(s): Homo sapiens
Expression System: Homo sapiens, Escherichia coli
Mutation(s): Yes
Membrane Protein: Yes mpstruc

Deposited: 2022-03-11 Released: 2022-08-03
Deposition Author(s): Miotto, M.C., 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: 2.97 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

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

PubMed: 35857850 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1126/sciadv.abo1272
Primary Citation 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. 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

Department of Physiology and Cellular Biophysics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA.

Macromolecule Content

Total Structure Weight: 2,379.79 kDa
Atom Count: 150,252
Modeled Residue Count: 18,768
Deposited Residue Count: 20,896
Unique protein chains: 3

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ryanodine receptor 2	A, J [auth B], K [auth C], L [auth D]	4,967	Homo sapiens	Mutation(s): 1 Gene Names: RYR2 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for Q92736 (Homo sapiens) Explore Q92736 Go to UniProtKB: Q92736
PHAROS: Q92736 GTEx: ENSG00000198626
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q92736
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptidyl-prolyl cis-trans isomerase FKBP1B	B [auth E], C [auth F], D [auth G], E [auth H]	108	Homo sapiens	Mutation(s): 0 Gene Names: FKBP1B, FKBP12.6, FKBP1L, FKBP9, OTK4 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 GTEx: ENSG00000119782
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P68106
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Calmodulin-1	F [auth I], G [auth J], H [auth K], I [auth L]	149	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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0DP23
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ATP (Subject of Investigation/LOI) Query on ATP Download:Ideal Coordinates CCD File SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain Q [auth B] SDF format, chain R [auth B] SDF format, chain T [auth C] SDF format, chain U [auth C] SDF format, chain W [auth D] SDF format, chain X [auth D] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] MOL2 format, chain T [auth C] MOL2 format, chain U [auth C] MOL2 format, chain W [auth D] MOL2 format, chain X [auth D] mmCIF format, chain N [auth A] mmCIF format, chain O [auth A] mmCIF format, chain Q [auth B] mmCIF format, chain R [auth B] mmCIF format, chain T [auth C] mmCIF format, chain U [auth C] mmCIF format, chain W [auth D] mmCIF format, chain X [auth D]	N [auth A] O [auth A] Q [auth B] R [auth B] T [auth C] N [auth A], O [auth A], Q [auth B], R [auth B], T [auth C], U [auth C], W [auth D], X [auth D]	ADENOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₃ P₃ ZKHQWZAMYRWXGA-KQYNXXCUSA-N		Interactions Focus chain N [auth A] Focus chain O [auth A] Focus chain Q [auth B] Focus chain R [auth B] Focus chain T [auth C] Focus chain U [auth C] Focus chain W [auth D] Focus chain X [auth D] Interactions & Density Focus chain N [auth A] Focus chain O [auth A] Focus chain Q [auth B] Focus chain R [auth B] Focus chain T [auth C] Focus chain U [auth C] Focus chain W [auth D] Focus chain X [auth D]
ZN (Subject of Investigation/LOI) Query on ZN Download:Ideal Coordinates CCD File SDF format, chain M [auth A] SDF format, chain P [auth B] SDF format, chain S [auth C] SDF format, chain V [auth D] MOL2 format, chain M [auth A] MOL2 format, chain P [auth B] MOL2 format, chain S [auth C] MOL2 format, chain V [auth D] mmCIF format, chain M [auth A] mmCIF format, chain P [auth B] mmCIF format, chain S [auth C] mmCIF format, chain V [auth D]	M [auth A], P [auth B], S [auth C], V [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain M [auth A] Focus chain P [auth B] Focus chain S [auth C] Focus chain V [auth D] Interactions & Density Focus chain M [auth A] Focus chain P [auth B] Focus chain S [auth C] Focus chain V [auth D]