9CGQ | pdb_00009cgq

Rabbit RyR1 disease mutant Y523S in complex with FKBP12.6, nanodisc and inhibitor dantrolene in the presence of activating calcium

PDB DOI: https://doi.org/10.2210/pdb9CGQ/pdb
EM Map EMD-45585: EMDB EMDataResource

Classification: MEMBRANE PROTEIN
Organism(s): Oryctolagus cuniculus, Homo sapiens
Expression System: Homo sapiens, Escherichia coli 'BL21-Gold(DE3)pLysS AG
Mutation(s): Yes

Deposited: 2024-06-30 Released: 2024-12-11
Deposition Author(s): Iyer, K.A., Samso, M.
Funding Organization(s): National Institutes of Health/National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIH/NIAMS), American Heart Association, Other private, National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.23 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Manuscript in preparation

Iyer, K.A., Kobayashi, T., Murayama, T., Samso, M.

To be published.

Macromolecule Content

Total Structure Weight: 2,313.71 kDa
Atom Count: 129,760
Modeled Residue Count: 17,048
Deposited Residue Count: 20,576
Unique protein chains: 2

Macromolecules

Find similar proteins by:

| 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): 1 Gene Names: RYR1
UniProt
Find proteins for P11716 (Oryctolagus cuniculus) Explore P11716 Go to UniProtKB: P11716
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P11716
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptidyl-prolyl cis-trans isomerase FKBP1B	E, F, G, H	107	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

Small Molecules

Ligands 4 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 V [auth D] SDF format, chain R [auth C] SDF format, chain N [auth B] SDF format, chain J [auth A] MOL2 format, chain V [auth D] MOL2 format, chain R [auth C] MOL2 format, chain N [auth B] MOL2 format, chain J [auth A] mmCIF format, chain V [auth D] mmCIF format, chain R [auth C] mmCIF format, chain N [auth B] mmCIF format, chain J [auth A]	J [auth A], N [auth B], R [auth C], V [auth D]	ADENOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₃ P₃ ZKHQWZAMYRWXGA-KQYNXXCUSA-N		Interactions Focus chain J [auth A] Focus chain N [auth B] Focus chain R [auth C] Focus chain V [auth D] Interactions & Density Focus chain J [auth A] Focus chain N [auth B] Focus chain R [auth C] Focus chain V [auth D]
U1C (Subject of Investigation/LOI) Query on U1C Download:Ideal Coordinates CCD File SDF format, chain X [auth D] SDF format, chain T [auth C] SDF format, chain P [auth B] SDF format, chain L [auth A] MOL2 format, chain X [auth D] MOL2 format, chain T [auth C] MOL2 format, chain P [auth B] MOL2 format, chain L [auth A] mmCIF format, chain X [auth D] mmCIF format, chain T [auth C] mmCIF format, chain P [auth B] mmCIF format, chain L [auth A]	L [auth A], P [auth B], T [auth C], X [auth D]	Dantrolene C₁₄ H₁₀ N₄ O₅ OZOMQRBLCMDCEG-CHHVJCJISA-N		Interactions Focus chain L [auth A] Focus chain P [auth B] Focus chain T [auth C] Focus chain X [auth D] Interactions & Density Focus chain L [auth A] Focus chain P [auth B] Focus chain T [auth C] Focus chain X [auth D]
ZN (Subject of Investigation/LOI) Query on ZN Download:Ideal Coordinates CCD File SDF format, chain U [auth D] SDF format, chain Q [auth C] SDF format, chain M [auth B] SDF format, chain I [auth A] MOL2 format, chain U [auth D] MOL2 format, chain Q [auth C] MOL2 format, chain M [auth B] MOL2 format, chain I [auth A] mmCIF format, chain U [auth D] mmCIF format, chain Q [auth C] mmCIF format, chain M [auth B] mmCIF format, chain I [auth A]	I [auth A], M [auth B], Q [auth C], U [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain M [auth B] Focus chain Q [auth C] Focus chain U [auth D] Interactions & Density Focus chain I [auth A] Focus chain M [auth B] Focus chain Q [auth C] Focus chain U [auth D]
CA (Subject of Investigation/LOI) Query on CA Download:Ideal Coordinates CCD File SDF format, chain W [auth D] SDF format, chain S [auth C] SDF format, chain O [auth B] SDF format, chain K [auth A] MOL2 format, chain W [auth D] MOL2 format, chain S [auth C] MOL2 format, chain O [auth B] MOL2 format, chain K [auth A] mmCIF format, chain W [auth D] mmCIF format, chain S [auth C] mmCIF format, chain O [auth B] mmCIF format, chain K [auth A]	K [auth A], O [auth B], S [auth C], W [auth D]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain K [auth A] Focus chain O [auth B] Focus chain S [auth C] Focus chain W [auth D] Interactions & Density Focus chain K [auth A] Focus chain O [auth B] Focus chain S [auth C] Focus chain W [auth D]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.23 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.20_4459:

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2024-12-11

Deposition Author(s):

Iyer, K.A.

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
American Heart Association	United States	19POST34430178
Other private		MDA 352845
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: 2024-12-11
Type: Initial release

9CGQ | pdb_00009cgq

Rabbit RyR1 disease mutant Y523S in complex with FKBP12.6, nanodisc and inhibitor dantrolene in the presence of activating calcium

Literature

Manuscript in preparation

Biological Assembly 1

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Expand

Entity ID: 2

UniProt & NIH Common Fund Data Resources