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TitleCryo-EM investigation of ryanodine receptor type 3.
Journal, issue, pagesNat Commun, Vol. 15, Issue 1, Page 8630, Year 2024
Publish dateOct 5, 2024
AuthorsYu Seby Chen / Maricela Garcia-Castañeda / Maria Charalambous / Daniela Rossi / Vincenzo Sorrentino / Filip Van Petegem /
PubMed AbstractRyanodine 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 ...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-induced Ca 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.
External linksNat Commun / PubMed:39366997 / PubMed Central
MethodsEM (single particle)
Resolution2.58 - 3.22 Å
Structure data

EMDB-45035: Consensus map of mink RyR3 in closed conformation
Method: EM (single particle) / Resolution: 2.89 Å

EMDB-45107: Local refinement map of mink RyR3 in closed conformation using mask 1 (FKBP12.6/NTD/Nsol/SPRY/Repeat1&2)
Method: EM (single particle) / Resolution: 2.7 Å

EMDB-45108: Local refinement map of mink RyR3 in closed conformation using mask 2 (Jsol/Csol/Bsol)
Method: EM (single particle) / Resolution: 2.71 Å

EMDB-45109: Local refinement map of mink RyR3 in closed conformation using mask 3 (Bsol/Repeat3&4)
Method: EM (single particle) / Resolution: 2.88 Å

EMDB-45110: Local refinement map of mink RyR3 in closed conformation using mask 4 (TMD/CTD)
Method: EM (single particle) / Resolution: 2.58 Å

EMDB-45111: Consensus map of mink RyR3 in open conformation bound to Ca2+/ATP/caffeine
Method: EM (single particle) / Resolution: 3.22 Å

EMDB-45112: Local refinement map of mink RyR3 in open conformation bound to Ca2+/ATP/caffeine using mask 1 (FKBP12.6/NTD/Nsol/SPRY/Repeat1&2)
Method: EM (single particle) / Resolution: 3.0 Å

EMDB-45113: Local refinement map of mink RyR3 in open conformation bound to Ca2+/ATP/caffeine using mask 2 (Jsol/Csol/Bsol)
Method: EM (single particle) / Resolution: 2.98 Å

EMDB-45114: Local refinement map of mink RyR3 in open conformation bound to Ca2+/ATP/caffeine using mask 3 (Bsol/Repeat3&4)
Method: EM (single particle) / Resolution: 3.2 Å

EMDB-45115: Local refinement map of mink RyR3 in open conformation bound to Ca2+/ATP/caffeine using mask 4 (TMD/CTD)
Method: EM (single particle) / Resolution: 2.99 Å

45116

9c1e

EMDB-45116: Composite map of mink RyR3 in closed conformation
PDB-9c1e: Mink RyR3 in closed conformation
Method: EM (single particle) / Resolution: 2.89 Å

45117

9c1f

EMDB-45117: Composite map of mink RyR3 in open conformation bound to Ca2+/ATP/caffeine
PDB-9c1f: Mink RyR3 in open conformation bound to Ca2+/ATP/caffeine
Method: EM (single particle) / Resolution: 3.22 Å

Chemicals

ChemComp-ZN:
Unknown entry

ChemComp-CL:
Unknown entry

ChemComp-CA:
Unknown entry

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM

ChemComp-CFF:
CAFFEINE / medication*YM

Source
  • neogale vison (American mink)
  • homo sapiens (human)
KeywordsMEMBRANE PROTEIN / RyR3 / Ryanodine Receptor / calcium channel / ion channel

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