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- PDB-9zlc: Structure of rabbit RyR1 RY12 domain complexed with ADP and Mg2+ -

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Basic information

Entry
Database: PDB / ID: 9zlc
TitleStructure of rabbit RyR1 RY12 domain complexed with ADP and Mg2+
ComponentsRyanodine receptor 1
KeywordsMEMBRANE PROTEIN / sarcoplasmic reticulum / intracellular calcium channel / excitation-contraction coupling / complex
Function / homology
Function and homology information


ATP-gated ion channel activity / ryanodine-sensitive calcium-release channel activity / terminal cisterna / release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / ossification involved in bone maturation / ryanodine receptor complex / cellular response to caffeine / skin development / organelle membrane / outflow tract morphogenesis ...ATP-gated ion channel activity / ryanodine-sensitive calcium-release channel activity / terminal cisterna / release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / ossification involved in bone maturation / ryanodine receptor complex / cellular response to caffeine / skin development / organelle membrane / outflow tract morphogenesis / smooth endoplasmic reticulum / intracellularly gated calcium channel activity / toxic substance binding / skeletal muscle fiber development / voltage-gated calcium channel activity / release of sequestered calcium ion into cytosol / cellular response to calcium ion / muscle contraction / sarcoplasmic reticulum membrane / sarcoplasmic reticulum / striated muscle contraction / sarcolemma / intracellular calcium ion homeostasis / Z disc / calcium channel activity / calcium ion transmembrane transport / disordered domain specific binding / protein homotetramerization / calmodulin binding / transmembrane transporter binding / calcium ion binding / ATP binding / membrane / identical protein binding
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 / 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 / Ion transport domain / Ion transport protein / EF-hand domain pair / Concanavalin A-like lectin/glucanase domain superfamily
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Ryanodine receptor 1
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.52 Å
AuthorsKim, K. / Clarke, O.B.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIH/NIAMS)R01AR077720 United States
CitationJournal: Nat Commun / Year: 2026
Title: Structural identification of the RY12 domain of RyR1 as an ADP sensor and the target of the malignant hyperthermia therapeutic dantrolene
Authors: Kim, K. / Li, H. / Yuan, Q. / Melville, Z. / Zalk, R. / des Georges, A. / Frank, J. / Hendrickson, W.A. / Marks, A.R. / Clarke, O.B.
History
DepositionDec 8, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 16, 2026Provider: repository / Type: Initial release
Revision 1.0Sep 16, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,6864
Polymers23,8071
Non-polymers8793
Water23413
1


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

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Components

#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: 23807.158 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: P11716
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 13 / Source method: isolated from a natural source / Formula: H2O
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

ComponentName: RyR1 complexed with FKBP12.6 and calmodulin / Type: COMPLEX / Entity ID: #1 / Source: NATURAL
Source (natural)Organism: Oryctolagus cuniculus (rabbit)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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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: 1500 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 58 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX1.21.2_5419:model refinement
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.52 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 612295 / Symmetry type: POINT
RefinementHighest resolution: 2.52 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.004146780
ELECTRON MICROSCOPYf_angle_d0.606198800
ELECTRON MICROSCOPYf_dihedral_angle_d7.39619991
ELECTRON MICROSCOPYf_chiral_restr0.04321892
ELECTRON MICROSCOPYf_plane_restr0.00525740

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