7UMZ | pdb_00007umz

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

PDB DOI: https://doi.org/10.2210/pdb7UMZ/pdb
EM Map EMD-26610: EMDB EMDataResource

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

Deposited: 2022-04-08 Released: 2023-04-12
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), 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: 3.09 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 2.2 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: 2,180.23 kDa
Atom Count: 111,396
Modeled Residue Count: 15,708
Deposited Residue Count: 20,148
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ryanodine receptor 1	A, B, C, D	5,037	Oryctolagus cuniculus	Mutation(s): 0

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
LBN Query on LBN Download:Ideal Coordinates CCD File SDF format, chain Z [auth C] SDF format, chain Y [auth C] SDF format, chain S [auth B] SDF format, chain R [auth B] SDF format, chain L [auth A] SDF format, chain K [auth A] SDF format, chain GA [auth D] SDF format, chain FA [auth D] MOL2 format, chain Z [auth C] MOL2 format, chain Y [auth C] MOL2 format, chain S [auth B] MOL2 format, chain R [auth B] MOL2 format, chain L [auth A] MOL2 format, chain K [auth A] MOL2 format, chain GA [auth D] MOL2 format, chain FA [auth D] mmCIF format, chain Z [auth C] mmCIF format, chain Y [auth C] mmCIF format, chain S [auth B] mmCIF format, chain R [auth B] mmCIF format, chain L [auth A] mmCIF format, chain K [auth A] mmCIF format, chain GA [auth D] mmCIF format, chain FA [auth D]	FA [auth D] GA [auth D] K [auth A] L [auth A] R [auth B] FA [auth D], GA [auth D], K [auth A], L [auth A], R [auth B], S [auth B], Y [auth C], Z [auth C]	1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine C₄₂ H₈₂ N O₈ P WTJKGGKOPKCXLL-VYOBOKEXSA-N		Interactions Focus chain FA [auth D] Focus chain GA [auth D] Focus chain K [auth A] Focus chain L [auth A] Focus chain R [auth B] Focus chain S [auth B] Focus chain Y [auth C] Focus chain Z [auth C] Interactions & Density Focus chain FA [auth D] Focus chain GA [auth D] Focus chain K [auth A] Focus chain L [auth A] Focus chain R [auth B] Focus chain S [auth B] Focus chain Y [auth C] Focus chain Z [auth C]
ACP Query on ACP Download:Ideal Coordinates CCD File SDF format, chain T [auth C] SDF format, chain M [auth B] SDF format, chain E [auth A] SDF format, chain AA [auth D] MOL2 format, chain T [auth C] MOL2 format, chain M [auth B] MOL2 format, chain E [auth A] MOL2 format, chain AA [auth D] mmCIF format, chain T [auth C] mmCIF format, chain M [auth B] mmCIF format, chain E [auth A] mmCIF format, chain AA [auth D]	AA [auth D], E [auth A], M [auth B], T [auth C]	PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER C₁₁ H₁₈ N₅ O₁₂ P₃ UFZTZBNSLXELAL-IOSLPCCCSA-N		Interactions Focus chain AA [auth D] Focus chain E [auth A] Focus chain M [auth B] Focus chain T [auth C] Interactions & Density Focus chain AA [auth D] Focus chain E [auth A] Focus chain M [auth B] Focus chain T [auth C]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain U [auth C] SDF format, chain N [auth B] SDF format, chain F [auth A] SDF format, chain BA [auth D] MOL2 format, chain U [auth C] MOL2 format, chain N [auth B] MOL2 format, chain F [auth A] MOL2 format, chain BA [auth D] mmCIF format, chain U [auth C] mmCIF format, chain N [auth B] mmCIF format, chain F [auth A] mmCIF format, chain BA [auth D]	BA [auth D], F [auth A], N [auth B], U [auth C]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain BA [auth D] Focus chain F [auth A] Focus chain N [auth B] Focus chain U [auth C] Interactions & Density Focus chain BA [auth D] Focus chain F [auth A] Focus chain N [auth B] Focus chain U [auth C]
MG (Subject of Investigation/LOI) Query on MG Download:Ideal Coordinates CCD File SDF format, chain EA [auth D] SDF format, chain X [auth C] SDF format, chain W [auth C] SDF format, chain V [auth C] SDF format, chain Q [auth B] SDF format, chain P [auth B] SDF format, chain O [auth B] SDF format, chain J [auth A] SDF format, chain I [auth A] SDF format, chain H [auth A] SDF format, chain G [auth A] SDF format, chain DA [auth D] SDF format, chain CA [auth D] MOL2 format, chain EA [auth D] MOL2 format, chain X [auth C] MOL2 format, chain W [auth C] MOL2 format, chain V [auth C] MOL2 format, chain Q [auth B] MOL2 format, chain P [auth B] MOL2 format, chain O [auth B] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain DA [auth D] MOL2 format, chain CA [auth D] mmCIF format, chain EA [auth D] mmCIF format, chain X [auth C] mmCIF format, chain W [auth C] mmCIF format, chain V [auth C] mmCIF format, chain Q [auth B] mmCIF format, chain P [auth B] mmCIF format, chain O [auth B] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain DA [auth D] mmCIF format, chain CA [auth D]	CA [auth D] DA [auth D] EA [auth D] G [auth A] H [auth A] CA [auth D], DA [auth D], EA [auth D], G [auth A], H [auth A], I [auth A], J [auth A], O [auth B], P [auth B], Q [auth B], V [auth C], W [auth C], X [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain CA [auth D] Focus chain DA [auth D] Focus chain EA [auth D] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain V [auth C] Focus chain W [auth C] Focus chain X [auth C] Interactions & Density Focus chain CA [auth D] Focus chain DA [auth D] Focus chain EA [auth D] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain V [auth C] Focus chain W [auth C] Focus chain X [auth C]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.09 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC	3.2
MODEL REFINEMENT	PHENIX	1.20rc4-4425

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2023-04-12

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 Institute of Arthritis and Musculoskeletal and Skin Diseases (NIH/NIAMS)	United States	R01 HL133182
Other private		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: 2023-04-12
Type: Initial release
Version 2.0: 2024-03-06
Type: Coordinate replacement
Reason: Polymer backbone linkage
Changes: Advisory, Atomic model, Author supporting evidence, Data collection, Database references, Derived calculations, Structure summary
Version 2.1: 2024-05-22
Changes: Database references
Version 2.2: 2024-10-30
Changes: Data collection, Structure summary