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- PDB-9yjv: Structure of RyR1-toxin complex -

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Basic information

Entry
Database: PDB / ID: 9yjv
TitleStructure of RyR1-toxin complex
Components
  • Peptidyl-prolyl cis-trans isomerase FKBP1B
  • Ryanodine receptor 1
KeywordsTRANSPORT PROTEIN/ISOMERASE/TOXIN / Ion channel / Complex / Activation / TRANSPORT PROTEIN-ISOMERASE-TOXIN complex
Function / homology
Function and homology information


negative regulation of calcium-mediated signaling / ATP-gated ion channel activity / negative regulation of release of sequestered calcium ion into cytosol / response to redox state / ryanodine-sensitive calcium-release channel activity / terminal cisterna / negative regulation of heart rate / release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / ossification involved in bone maturation / cellular response to caffeine ...negative regulation of calcium-mediated signaling / ATP-gated ion channel activity / negative regulation of release of sequestered calcium ion into cytosol / response to redox state / ryanodine-sensitive calcium-release channel activity / terminal cisterna / negative regulation of heart rate / release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / ossification involved in bone maturation / cellular response to caffeine / skin development / ryanodine receptor complex / FK506 binding / 'de novo' protein folding / organelle membrane / outflow tract morphogenesis / smooth endoplasmic reticulum / intracellularly gated calcium channel activity / regulation of ryanodine-sensitive calcium-release channel activity / toxic substance binding / calcium channel inhibitor activity / skeletal muscle fiber development / voltage-gated calcium channel activity / release of sequestered calcium ion into cytosol / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / Ion homeostasis / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / calcium channel complex / cellular response to calcium ion / muscle contraction / sarcoplasmic reticulum membrane / calcium-mediated signaling / calcium channel regulator activity / peptidylprolyl isomerase / sarcoplasmic reticulum / peptidyl-prolyl cis-trans isomerase activity / striated muscle contraction / protein refolding / sarcolemma / intracellular calcium ion homeostasis / protein maturation / calcium channel activity / Z disc / Stimuli-sensing channels / calcium ion transmembrane transport / disordered domain specific binding / protein folding / calmodulin binding / protein homotetramerization / transmembrane transporter binding / signaling receptor binding / calcium ion binding / ATP binding / membrane / identical protein binding / cytoplasm
Similarity search - Function
Ryanodine receptor, SPRY domain 2 / : / Ryanodine receptor junctional solenoid repeat / Ryanodine Receptor TM 4-6 / Ryanodine receptor / Ryanodine receptor, SPRY domain 1 / Ryanodine receptor, SPRY domain 3 / Ryanodine Receptor TM 4-6 / Ryanodine receptor Ryr / RyR domain ...Ryanodine receptor, SPRY domain 2 / : / Ryanodine receptor junctional solenoid repeat / Ryanodine Receptor TM 4-6 / Ryanodine receptor / Ryanodine receptor, SPRY domain 1 / Ryanodine receptor, SPRY domain 3 / Ryanodine Receptor TM 4-6 / Ryanodine receptor Ryr / RyR domain / : / RyR/IP3 receptor binding core, RIH domain superfamily / RyR/IP3R Homology associated domain / Inositol 1,4,5-trisphosphate/ryanodine receptor / RIH domain / RyR and IP3R Homology associated / Inositol 1,4,5-trisphosphate/ryanodine receptor / RIH domain / : / MIR motif / MIR domain / MIR domain profile. / Domain in ryanodine and inositol trisphosphate receptors and protein O-mannosyltransferases / Mir domain superfamily / FKBP-type peptidyl-prolyl cis-trans isomerase / FKBP-type peptidyl-prolyl cis-trans isomerase domain / FKBP-type peptidyl-prolyl cis-trans isomerase domain profile. / SPRY domain / B30.2/SPRY domain / B30.2/SPRY domain profile. / B30.2/SPRY domain superfamily / Domain in SPla and the RYanodine Receptor. / SPRY domain / Peptidyl-prolyl cis-trans isomerase domain superfamily / Ion transport domain / Ion transport protein / EF-hand domain pair / Concanavalin A-like lectin/glucanase domain superfamily
Similarity search - Domain/homology
: / ADENOSINE-5'-TRIPHOSPHATE / CAFFEINE / Ryanodine receptor 1 / Peptidyl-prolyl cis-trans isomerase FKBP1B
Similarity search - Component
Biological speciesHomo sapiens (human)
Oryctolagus cuniculus (rabbit)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.87 Å
AuthorsZhang, Y. / Yuchi, Z. / Van Petegem, F.
Funding support Canada, China, 2items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)PJT-159601 Canada
Chinese Scholarship Council202306250027 China
CitationJournal: To Be Published
Title: Structure of RyR1-toxin complex
Authors: Zhang, Y. / Yuchi, Z. / Van Petegem, F.
History
DepositionOct 5, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 7, 2026Provider: repository / Type: Initial release
Revision 1.0Oct 7, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ryanodine receptor 1
B: Peptidyl-prolyl cis-trans isomerase FKBP1B
C: Peptidyl-prolyl cis-trans isomerase FKBP1B
D: Ryanodine receptor 1
E: Peptidyl-prolyl cis-trans isomerase FKBP1B
F: Ryanodine receptor 1
G: Peptidyl-prolyl cis-trans isomerase FKBP1B
H: Ryanodine receptor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,314,83728
Polymers2,310,3048
Non-polymers4,53320
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 2 types, 8 molecules ADFHBCEG

#1: Protein
Ryanodine receptor 1 / RYR-1 / RyR1 / Skeletal muscle calcium release channel / Skeletal muscle ryanodine receptor / ...RYR-1 / RyR1 / Skeletal muscle calcium release channel / Skeletal muscle ryanodine receptor / Skeletal muscle-type ryanodine receptor / Type 1 ryanodine receptor


Mass: 565908.625 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: P11716
#2: Protein
Peptidyl-prolyl cis-trans isomerase FKBP1B / PPIase FKBP1B / 12.6 kDa FK506-binding protein / FKBP-12.6 / FK506-binding protein 1B / FKBP-1B / ...PPIase FKBP1B / 12.6 kDa FK506-binding protein / FKBP-12.6 / FK506-binding protein 1B / FKBP-1B / Immunophilin FKBP12.6 / Rotamase / h-FKBP-12


Mass: 11667.305 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FKBP1B, FKBP12.6, FKBP1L, FKBP9, OTK4 / Production host: Escherichia coli (E. coli) / References: UniProt: P68106, peptidylprolyl isomerase

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Non-polymers , 5 types, 20 molecules

#3: Chemical
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#4: Chemical
ChemComp-CFF / CAFFEINE / 3,7-DIHYDRO-1,3,7-TRIMETHYL-1H-PURINE-2,6-DIONE


Mass: 194.191 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H10N4O2 / Comment: medication*YM
#5: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#6: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#7: Chemical
ChemComp-A1CXI / (1P)-2,2',3,5',6-pentachloro-1,1'-biphenyl


Mass: 326.433 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C12H5Cl5 / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1Complex between Ryanodine Receptor 1 and FKBP12.6COMPLEX#1-#20MULTIPLE SOURCES
2Ryanodine receptor 1COMPLEX#11NATURAL
3Peptidyl-prolyl cis-trans isomerase FKBP1BCOMPLEX#21RECOMBINANT
Molecular weight
IDEntity assembly-IDValue (°)Experimental value
112 MDaNO
212 MDaNO
310.011 MDaNO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
42Oryctolagus cuniculus (rabbit)9986
53Homo sapiens (human)9606
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
SpecimenConc.: 12 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: 50 mM HEPES pH 7.5 + 500 mM NaCl + 2 mM EGTA + 2 mM TCEP + 0.1 mM PMSF + 0.5% CHAPS + 0.2% soybean phosphatidylcholine + 1:1000 protease inhibitor cocktail
Specimen supportGrid type: Quantifoil R2/2
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 8121

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.6.2particle selection
2PHENIX1.21.2_5419:model refinement
5cryoSPARC4.6.2CTF correction
11cryoSPARC4.6.2final Euler assignment
13cryoSPARC4.6.23D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 343385
SymmetryPoint symmetry: C4 (4 fold cyclic)
3D reconstructionResolution: 2.87 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 185628 / Symmetry type: POINT

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