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- PDB-9yn4: Structure of mouse RyR1 mutant T4706M (Ca2+/CFF/ATP dataset; open... -

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Basic information

Entry
Database: PDB / ID: 9yn4
TitleStructure of mouse RyR1 mutant T4706M (Ca2+/CFF/ATP dataset; open pore)
Components
  • Peptidyl-prolyl cis-trans isomerase FKBP1A
  • Ryanodine receptor 1
KeywordsTRANSPORT PROTEIN/ISOMERASE / Calcium / Ion Channel / Membrane Protein / TRANSPORT PROTEIN-ISOMERASE complex
Function / homology
Function and homology information


regulation of response to osmotic stress / TGF-beta receptor signaling activates SMADs / junctional membrane complex / Calcineurin activates NFAT / mTORC1-mediated signalling / sarcoplasmic reticulum calcium ion transport / activin receptor binding / calcium-induced calcium release activity / regulation of muscle contraction / transforming growth factor beta receptor binding ...regulation of response to osmotic stress / TGF-beta receptor signaling activates SMADs / junctional membrane complex / Calcineurin activates NFAT / mTORC1-mediated signalling / sarcoplasmic reticulum calcium ion transport / activin receptor binding / calcium-induced calcium release activity / regulation of muscle contraction / transforming growth factor beta receptor binding / heart trabecula formation / Stimuli-sensing channels / type I transforming growth factor beta receptor binding / signaling receptor inhibitor activity / Ion homeostasis / T cell proliferation / cytoplasmic side of membrane / I-SMAD binding / response to caffeine / ryanodine-sensitive calcium-release channel activity / terminal cisterna / I band / release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / ossification involved in bone maturation / extrinsic component of cytoplasmic side of plasma membrane / cellular response to caffeine / skin development / ventricular cardiac muscle tissue morphogenesis / ryanodine receptor complex / FK506 binding / organelle membrane / outflow tract morphogenesis / cellular response to ATP / smooth endoplasmic reticulum / heart morphogenesis / regulation of cytosolic calcium ion concentration / skeletal muscle fiber development / release of sequestered calcium ion into cytosol / voltage-gated calcium channel activity / 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 / T-tubule / negative regulation of transforming growth factor beta receptor signaling pathway / Hsp70 protein binding / axon terminus / sarcomere / calcium channel regulator activity / peptidylprolyl isomerase / sarcoplasmic reticulum / peptidyl-prolyl cis-trans isomerase activity / striated muscle contraction / sarcolemma / calcium channel activity / Z disc / cytokine-mediated signaling pathway / calcium ion transmembrane transport / calcium ion transport / protein folding / protease binding / cell cortex / response to hypoxia / vesicle / protein homotetramerization / cytoplasmic side of plasma membrane / transmembrane transporter binding / calcium ion binding / synapse / perinuclear region of cytoplasm / enzyme binding / protein-containing complex / ATP binding / membrane / identical protein binding / plasma membrane / cytosol / 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 / 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / Ryanodine receptor 1 / Peptidyl-prolyl cis-trans isomerase FKBP1A
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsWeninger, G. / Marks, A.R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)R01 HL145473 United States
CitationJournal: To Be Published
Title: Structural basis for increased activity of an RyR1 mutant channel linked to skeletal myopathy
Authors: Weninger, G.
History
DepositionOct 10, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 21, 2026Provider: repository / Type: Initial release
Revision 1.0Oct 21, 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
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
C: Ryanodine receptor 1
A: Ryanodine receptor 1
D: Ryanodine receptor 1
B: Ryanodine receptor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,322,20236
Polymers2,310,6498
Non-polymers11,55328
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 EFGHCADB

#1: 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: 11939.629 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P26883, peptidylprolyl isomerase
#2: 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: 565722.625 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: E9PZQ0

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Non-polymers , 5 types, 28 molecules

#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#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-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#6: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#7: Chemical
ChemComp-PCW / 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / (Z,Z)-4-HYDROXY-N,N,N-TRIMETHYL-10-OXO-7-[(1-OXO-9-OCTADECENYL)OXY]-3,5,9-TRIOXA-4-PHOSPHAHEPTACOS-18-EN-1-AMINIUM-4-OXIDE


Mass: 787.121 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C44H85NO8P / Comment: DOPC, phospholipid*YM

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Details

Has ligand of interestN
Has protein modificationY

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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

ComponentName: Complex of RyR1 mutant T4706M with Calstabin-1 (Ca2+/CFF/ATP condition)
Type: COMPLEX / Details: 0.03 mM free Ca2+; 5 mM Caffeine; 10 mM ATP / Entity ID: #2, #1 / Source: NATURAL
Source (natural)Organism: Mus musculus (house mouse)
Buffer solutionpH: 7.4
Buffer component
IDConc.NameFormulaBuffer-ID
110 mmol/LHEPES1
2400 mmol/Lsodium chlorideNaCl1
31 mmol/LEDTA1
40.25 %CHAPS1
50.01 %DOPC1
60.5 mmol/LTCEP1
SpecimenConc.: 8.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
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: 1200 nm / Nominal defocus min: 500 nm / Cs: 2.7 mm / C2 aperture diameter: 100 µm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 58 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 6469

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
7Cootmodel fitting
9cryoSPARCinitial Euler assignment
10cryoSPARCfinal Euler assignment
11cryoSPARCclassification
12cryoSPARC3D reconstruction
13PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 48780 / Symmetry type: POINT
RefinementHighest resolution: 3.4 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.004146488
ELECTRON MICROSCOPYf_angle_d0.599198380
ELECTRON MICROSCOPYf_dihedral_angle_d6.99719884
ELECTRON MICROSCOPYf_chiral_restr0.03821740
ELECTRON MICROSCOPYf_plane_restr0.00525732

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