7K0S | pdb_00007k0s

Cryo-EM structure of rabbit RyR1 in the presence of Mg2+ and AMP-PCP in nanodisc

PDB DOI: https://doi.org/10.2210/pdb7K0S/pdb
EM Map EMD-22615: EMDB EMDataResource

Classification: TRANSPORT PROTEIN
Organism(s): Oryctolagus cuniculus
Mutation(s): No

Deposited: 2020-09-05 Released: 2021-09-22
Deposition Author(s): Nayak, A.R., Samso, M.
Funding Organization(s): National Institutes of Health/National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIH/NIAMS), National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI), Other private, National Institutes of Health/National Cancer Institute (NIH/NCI), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 4.50 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 2.3 of the entry. See complete history.

Literature

Interplay between Mg2+ and Ca2+ at multiple sites of the ryanodine receptor

Nayak, A.R., Rangubpit, W., Will, A.H., Hu, Y., Castro-Hartmann, P., Lobo, J.J., Dryden, K., Lamb, G.D., Sompornpisut, P., Samso, M.

(2024) Nat Commun 15: 4115

DOI: https://doi.org/10.1038/s41467-024-48292-3

Macromolecule Content

Total Structure Weight: 2,137.06 kDa
Atom Count: 115,935
Modeled Residue Count: 16,440
Deposited Residue Count: 20,148
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RyR1	A, B, C [auth D], D [auth C]	5,037	Oryctolagus cuniculus	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ACP Query on ACP Download Ideal Coordinates CCD File SDF format, chain O [auth C] SDF format, chain L [auth D] SDF format, chain H [auth B] SDF format, chain E [auth A] MOL2 format, chain O [auth C] MOL2 format, chain L [auth D] MOL2 format, chain H [auth B] MOL2 format, chain E [auth A] mmCIF format, chain O [auth C] mmCIF format, chain L [auth D] mmCIF format, chain H [auth B] mmCIF format, chain E [auth A]	E [auth A], H [auth B], L [auth D], O [auth C]	PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER C₁₁ H₁₈ N₅ O₁₂ P₃ UFZTZBNSLXELAL-IOSLPCCCSA-N		Interactions Focus chain E [auth A] Focus chain H [auth B] Focus chain L [auth D] Focus chain O [auth C] Interactions & Density Focus chain E [auth A] Focus chain H [auth B] Focus chain L [auth D] Focus chain O [auth C]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain P [auth C] SDF format, chain M [auth D] SDF format, chain I [auth B] SDF format, chain F [auth A] MOL2 format, chain P [auth C] MOL2 format, chain M [auth D] MOL2 format, chain I [auth B] MOL2 format, chain F [auth A] mmCIF format, chain P [auth C] mmCIF format, chain M [auth D] mmCIF format, chain I [auth B] mmCIF format, chain F [auth A]	F [auth A], I [auth B], M [auth D], P [auth C]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain I [auth B] Focus chain M [auth D] Focus chain P [auth C] Interactions & Density Focus chain F [auth A] Focus chain I [auth B] Focus chain M [auth D] Focus chain P [auth C]
MG (Subject of Investigation/LOI) Query on MG Download Ideal Coordinates CCD File SDF format, chain Q [auth C] SDF format, chain N [auth D] SDF format, chain K [auth B] SDF format, chain J [auth B] SDF format, chain G [auth A] MOL2 format, chain Q [auth C] MOL2 format, chain N [auth D] MOL2 format, chain K [auth B] MOL2 format, chain J [auth B] MOL2 format, chain G [auth A] mmCIF format, chain Q [auth C] mmCIF format, chain N [auth D] mmCIF format, chain K [auth B] mmCIF format, chain J [auth B] mmCIF format, chain G [auth A]	G [auth A], J [auth B], K [auth B], N [auth D], Q [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain N [auth D] Focus chain Q [auth C] Interactions & Density Focus chain G [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain N [auth D] Focus chain Q [auth C]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 4.50 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	dev-3958-000
RECONSTRUCTION	RELION	1.4

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2021-09-22

Deposition Author(s):

Nayak, A.R.

Samso, M.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIH/NIAMS)	United States	R01 AR068431
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)	United States	R01 HL133182
Other private	United States	MDA 352845
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	HSSN261200800001E
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	U24 GM116789
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	U24 GM116790

Revision History (Full details and data files)

Version 1.0: 2021-09-22
Type: Initial release
Version 2.0: 2022-03-09
Type: Coordinate replacement
Reason: Polymer backbone linkage
Changes: Advisory, Atomic model, Author supporting evidence, Data collection, Database references, Derived calculations, Experimental preparation, Polymer sequence, Source and taxonomy, Structure summary
Version 2.1: 2024-02-28
Changes: Data collection, Database references
Version 2.2: 2024-05-22
Changes: Database references
Version 2.3: 2024-11-20
Changes: Data collection, Structure summary