9C1F | pdb_00009c1f

Mink RyR3 in open conformation bound to Ca2+/ATP/caffeine

PDB DOI: https://doi.org/10.2210/pdb9C1F/pdb
EM Map EMD-45117: EMDB EMDataResource

Classification: MEMBRANE PROTEIN
Organism(s): Homo sapiens, Neogale vison
Expression System: Escherichia coli BL21(DE3), Homo sapiens
Mutation(s): No

Deposited: 2024-05-29 Released: 2024-10-16
Deposition Author(s): Chen, Y.S., Van Petegem, F.
Funding Organization(s): Canadian Institutes of Health Research (CIHR), Fonds de Recherche du Quebec - Sante (FRQS), Other government

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.22 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

Cryo-EM investigation of ryanodine receptor type 3.

Chen, Y.S., Garcia-Castaneda, M., Charalambous, M., Rossi, D., Sorrentino, V., Van Petegem, F.

(2024) Nat Commun 15: 8630-8630

PubMed: 39366997 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1038/s41467-024-52998-9
Primary Citation of Related Structures:
9C1E, 9C1F

PubMed Abstract:
Ryanodine Receptor isoform 3 (RyR3) is a large ion channel found in the endoplasmic reticulum membrane of many different cell types. Within the hippocampal region of the brain, it is found in dendritic spines and regulates synaptic plasticity. It controls myogenic tone in arteries and is upregulated in skeletal muscle in early development. RyR3 has a unique functional profile with a very high sensitivity to activating ligands, enabling high gain in Ca ²⁺-induced Ca ²⁺ release. Here we solve high-resolution cryo-EM structures of RyR3 in non-activating and activating conditions, revealing structural transitions that occur during channel opening. Addition of activating ligands yields only open channels, indicating an intrinsically high open probability under these conditions. RyR3 has reduced binding affinity to the auxiliary protein FKBP12.6 due to several sequence variations in the binding interface. We map disease-associated sequence variants and binding sites for known pharmacological agents. The N-terminal region contains ligand binding sites for a putative chloride anion and ATP, both of which are targeted by sequence variants linked to epileptic encephalopathy.

Organizational Affiliation

Department of Biochemistry and Molecular Biology, the Life Sciences Centre, University of British Columbia, Vancouver, BC, Canada.

Macromolecule Content

Total Structure Weight: 2,258.03 kDa
Atom Count: 130,372
Modeled Residue Count: 16,736
Deposited Residue Count: 19,876
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptidyl-prolyl cis-trans isomerase FKBP1B	A, C, E, G	110	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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P68106
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Ryanodine receptor 3	B, D, F, H	4,859	Neogale vison	Mutation(s): 0 Gene Names: RYR3
UniProt
Find proteins for A0A8C7B9Y8 (Neovison vison) Explore A0A8C7B9Y8 Go to UniProtKB: A0A8C7B9Y8
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A8C7B9Y8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 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 CA [auth H] SDF format, chain EA [auth H] SDF format, chain K [auth B] SDF format, chain M [auth B] SDF format, chain Q [auth D] SDF format, chain S [auth D] SDF format, chain W [auth F] SDF format, chain Y [auth F] MOL2 format, chain CA [auth H] MOL2 format, chain EA [auth H] MOL2 format, chain K [auth B] MOL2 format, chain M [auth B] MOL2 format, chain Q [auth D] MOL2 format, chain S [auth D] MOL2 format, chain W [auth F] MOL2 format, chain Y [auth F] mmCIF format, chain CA [auth H] mmCIF format, chain EA [auth H] mmCIF format, chain K [auth B] mmCIF format, chain M [auth B] mmCIF format, chain Q [auth D] mmCIF format, chain S [auth D] mmCIF format, chain W [auth F] mmCIF format, chain Y [auth F]	CA [auth H] EA [auth H] K [auth B] M [auth B] Q [auth D] CA [auth H], EA [auth H], K [auth B], M [auth B], Q [auth D], S [auth D], W [auth F], Y [auth F]	ADENOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₃ P₃ ZKHQWZAMYRWXGA-KQYNXXCUSA-N		Interactions Focus chain CA [auth H] Focus chain EA [auth H] Focus chain K [auth B] Focus chain M [auth B] Focus chain Q [auth D] Focus chain S [auth D] Focus chain W [auth F] Focus chain Y [auth F] Interactions & Density Focus chain CA [auth H] Focus chain EA [auth H] Focus chain K [auth B] Focus chain M [auth B] Focus chain Q [auth D] Focus chain S [auth D] Focus chain W [auth F] Focus chain Y [auth F]
CFF (Subject of Investigation/LOI) Query on CFF Download Ideal Coordinates CCD File SDF format, chain DA [auth H] SDF format, chain X [auth F] SDF format, chain L [auth B] SDF format, chain R [auth D] MOL2 format, chain DA [auth H] MOL2 format, chain X [auth F] MOL2 format, chain L [auth B] MOL2 format, chain R [auth D] mmCIF format, chain DA [auth H] mmCIF format, chain X [auth F] mmCIF format, chain L [auth B] mmCIF format, chain R [auth D]	DA [auth H], L [auth B], R [auth D], X [auth F]	CAFFEINE C₈ H₁₀ N₄ O₂ RYYVLZVUVIJVGH-UHFFFAOYSA-N		Interactions Focus chain DA [auth H] Focus chain L [auth B] Focus chain R [auth D] Focus chain X [auth F] Interactions & Density Focus chain DA [auth H] Focus chain L [auth B] Focus chain R [auth D] Focus chain X [auth F]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain O [auth D] SDF format, chain U [auth F] SDF format, chain AA [auth H] MOL2 format, chain I [auth B] MOL2 format, chain O [auth D] MOL2 format, chain U [auth F] MOL2 format, chain AA [auth H] mmCIF format, chain I [auth B] mmCIF format, chain O [auth D] mmCIF format, chain U [auth F] mmCIF format, chain AA [auth H]	AA [auth H], I [auth B], O [auth D], U [auth F]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain AA [auth H] Focus chain I [auth B] Focus chain O [auth D] Focus chain U [auth F] Interactions & Density Focus chain AA [auth H] Focus chain I [auth B] Focus chain O [auth D] Focus chain U [auth F]
CA (Subject of Investigation/LOI) Query on CA Download Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain V [auth F] SDF format, chain BA [auth H] SDF format, chain P [auth D] MOL2 format, chain J [auth B] MOL2 format, chain V [auth F] MOL2 format, chain BA [auth H] MOL2 format, chain P [auth D] mmCIF format, chain J [auth B] mmCIF format, chain V [auth F] mmCIF format, chain BA [auth H] mmCIF format, chain P [auth D]	BA [auth H], J [auth B], P [auth D], V [auth F]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain BA [auth H] Focus chain J [auth B] Focus chain P [auth D] Focus chain V [auth F] Interactions & Density Focus chain BA [auth H] Focus chain J [auth B] Focus chain P [auth D] Focus chain V [auth F]
CL (Subject of Investigation/LOI) Query on CL Download Ideal Coordinates CCD File SDF format, chain FA [auth H] SDF format, chain N [auth B] SDF format, chain T [auth D] SDF format, chain Z [auth F] MOL2 format, chain FA [auth H] MOL2 format, chain N [auth B] MOL2 format, chain T [auth D] MOL2 format, chain Z [auth F] mmCIF format, chain FA [auth H] mmCIF format, chain N [auth B] mmCIF format, chain T [auth D] mmCIF format, chain Z [auth F]	FA [auth H], N [auth B], T [auth D], Z [auth F]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain FA [auth H] Focus chain N [auth B] Focus chain T [auth D] Focus chain Z [auth F] Interactions & Density Focus chain FA [auth H] Focus chain N [auth B] Focus chain T [auth D] Focus chain Z [auth F]