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- PDB-9s5z: Primed-state RyR1 with activating ligand mixture (Calcium/ACP/Caf... -

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Basic information

Entry
Database: PDB / ID: 9s5z
TitlePrimed-state RyR1 with activating ligand mixture (Calcium/ACP/Caffeine) in the native membrane solved by StA
Components
  • Peptidyl-prolyl cis-trans isomerase FKBP1A
  • Ryanodine receptor 1
KeywordsMEMBRANE PROTEIN / ryanodine receptor type 1 / ryr1 / skeletal muscle / sarcoplasmic reticulum / SR / native membrane
Function / homology
Function and homology information


cytoplasmic side of membrane / ATP-gated ion channel activity / ryanodine-sensitive calcium-release channel activity / terminal cisterna / ryanodine receptor complex / release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / ossification involved in bone maturation / skin development / cellular response to caffeine / outflow tract morphogenesis ...cytoplasmic side of membrane / ATP-gated ion channel activity / ryanodine-sensitive calcium-release channel activity / terminal cisterna / ryanodine receptor complex / release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / ossification involved in bone maturation / skin development / cellular response to caffeine / outflow tract morphogenesis / organelle membrane / smooth endoplasmic reticulum / intracellularly gated calcium channel activity / intracellular membrane-bounded organelle / regulation of ryanodine-sensitive calcium-release channel activity / toxic substance binding / 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 / muscle contraction / cellular response to calcium ion / sarcoplasmic reticulum membrane / peptidylprolyl isomerase / sarcoplasmic reticulum / striated muscle contraction / peptidyl-prolyl cis-trans isomerase activity / sarcolemma / intracellular calcium ion homeostasis / Z disc / calcium ion transmembrane transport / calcium channel activity / disordered domain specific binding / protein homotetramerization / transmembrane transporter binding / calmodulin binding / calcium ion binding / ATP binding / membrane / identical protein binding / cytosol
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
PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / CAFFEINE / Ryanodine receptor 1 / Peptidyl-prolyl cis-trans isomerase FKBP1A
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodELECTRON MICROSCOPY / subtomogram averaging / cryo EM / Resolution: 4.43 Å
AuthorsMikirtumov, V.
Funding support Germany, 2items
OrganizationGrant numberCountry
German Research Foundation (DFG)KU3221/3-1 Germany
Helmholtz Association Germany
CitationJournal: To Be Published
Title: Activation of RyR1 in native membranes
Authors: Mikirtumov, V. / Golusik, S. / Sprink, T. / Balyschew, N. / Yang, W. / Kotecha, A. / Kudryashev, M.
History
DepositionJul 30, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 12, 2026Provider: repository / Type: Initial release
Revision 1.0Aug 12, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Aug 12, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Aug 12, 2026Data content type: Primary map / Data content type: Primary map / 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: Ryanodine receptor 1
C: Ryanodine receptor 1
D: Ryanodine receptor 1
E: Peptidyl-prolyl cis-trans isomerase FKBP1A
F: Peptidyl-prolyl cis-trans isomerase FKBP1A
G: Peptidyl-prolyl cis-trans isomerase FKBP1A
H: Peptidyl-prolyl cis-trans isomerase FKBP1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,314,72524
Polymers2,311,5058
Non-polymers3,22016
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Protein , 2 types, 8 molecules ABCDEFGH

#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 FKBP1A / PPIase FKBP1A / 12 kDa FK506-binding protein / 12 kDa FKBP / FKBP-12 / Calstabin-1 / FK506-binding ...PPIase FKBP1A / 12 kDa FK506-binding protein / 12 kDa FKBP / FKBP-12 / Calstabin-1 / FK506-binding protein 1A / FKBP-1A / Immunophilin FKBP12 / Rotamase


Mass: 11967.705 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: P62943, peptidylprolyl isomerase

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Non-polymers , 4 types, 16 molecules

#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-ACP / PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / ADENOSINE-5'-[BETA, GAMMA-METHYLENE]TRIPHOSPHATE


Mass: 505.208 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C11H18N5O12P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP-PCP, energy-carrying molecule analogue*YM
#6: 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 / Feature type: SUBJECT OF INVESTIGATION / Comment: medication*YM

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Details

Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: subtomogram averaging

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Sample preparation

ComponentName: Ryanodine receptor type 1 in complex with FKBP12 in the sarcoplasmic reticulum membrane
Type: ORGANELLE OR CELLULAR COMPONENT
Details: Sarcoplasmic reticulum membrane vesicles purified from the native skeletal muscle tissue
Entity ID: #1-#2 / Source: NATURAL
Molecular weightValue: 2.2 MDa / Experimental value: NO
Source (natural)Organism: Oryctolagus cuniculus (rabbit) / Organ: hind leg and back / Organelle: sarcoplasmic reticulum / Tissue: skeletal muscle
Buffer solutionpH: 7.1
SpecimenConc.: 29.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 200 divisions/in. / Grid type: UltrAuFoil R2/2
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 95 % / 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 magnification: 64000 X / Calibrated magnification: 64000 X / Nominal defocus max: 7000 nm / Nominal defocus min: 2000 nm / Calibrated defocus min: 2000 nm / Calibrated defocus max: 7000 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 2 sec. / Electron dose: 4.17 e/Å2 / Avg electron dose per subtomogram: 117 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of real images: 1
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV
Image scansWidth: 11520 / Height: 8184

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Processing

EM software
IDNameVersionCategory
1PyTomvolume selection
2SerialEMimage acquisition
4GctfCTF correction
5IMODCTF correction
6RELION4CTF correction
9UCSF ChimeraXmodel fitting
11ISOLDEmodel refinement
12PHENIXmodel refinement
13cryoSPARC4.6.0initial Euler assignment
14RELION4final Euler assignment
15RELION4classification
16RELION43D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 2171564
SymmetryPoint symmetry: C4 (4 fold cyclic)
3D reconstructionResolution: 4.43 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 13358 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT
EM volume selectionMethod: pyTOM Template Matching / Num. of tomograms: 182 / Num. of volumes extracted: 524185 / Reference model: EMD-17272
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Atomic model buildingPDB-ID: 7tzc

7tzc


Accession code: 7tzc / Source name: PDB / Type: experimental model

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