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- EMDB-74403: Structure of RY12 domain of rabbit RyR1 complexed with dantrolene... -

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Basic information

Entry
Database: EMDB / ID: EMD-74403
TitleStructure of RY12 domain of rabbit RyR1 complexed with dantrolene and ADP
Map data
Sample
  • Complex: RyR1 complexed with FKBP12.6 and calmodulin
    • Protein or peptide: Ryanodine receptor 1
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: Dantrolene
  • Ligand: water
Keywordssarcoplasmic reticulum / intracellular calcium channel / excitation-contraction coupling / complex / MEMBRANE PROTEIN
Function / homology
Function and homology information


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 ...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 / toxic substance binding / skeletal muscle fiber development / voltage-gated calcium channel activity / release of sequestered calcium ion into cytosol / muscle contraction / cellular response to calcium ion / 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
Ryanodine receptor 1
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.14 Å
AuthorsKim K / Clarke OB
Funding support United States, 1 items
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 WA / Marks AR / Clarke OB
History
DepositionDec 8, 2025-
Header (metadata) releaseSep 16, 2026-
Map releaseSep 16, 2026-
UpdateSep 16, 2026-
Current statusSep 16, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_74403.png

Downloads & links

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Map

FileDownload / File: emd_74403.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 256 pix.
= 212.48 Å		0.83 Å/pix.
x 256 pix.
= 212.48 Å		0.83 Å/pix.
x 256 pix.
= 212.48 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.8
Minimum - Maximum-4.247242 - 6.2483664
Average (Standard dev.)0.012096926 (±0.10596998)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 212.48 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_74403_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_74403_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_74403_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : RyR1 complexed with FKBP12.6 and calmodulin

EntireName: RyR1 complexed with FKBP12.6 and calmodulin
Components
  • Complex: RyR1 complexed with FKBP12.6 and calmodulin
    • Protein or peptide: Ryanodine receptor 1
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: Dantrolene
  • Ligand: water

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Supramolecule #1: RyR1 complexed with FKBP12.6 and calmodulin

SupramoleculeName: RyR1 complexed with FKBP12.6 and calmodulin / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Oryctolagus cuniculus (rabbit)

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Macromolecule #1: Ryanodine receptor 1

MacromoleculeName: Ryanodine receptor 1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Oryctolagus cuniculus (rabbit)
Molecular weightTheoretical: 23.594955 KDa
SequenceString: DFVPCPVDTV QIVLPPHLER IREKLAENIH ELWALTRIEQ GWTYGPVRDD NKRLHPCLVN FHSLPEPERN YNLQMSGETL KTLLALGCH VGMADEKAED NLKKTKLPKT YMMSNGYKPA PLDLSHVRLT PAQTTLVDRL AENGHNVWAR DRVAQGWSYS A VQDIPARR ...String:
DFVPCPVDTV QIVLPPHLER IREKLAENIH ELWALTRIEQ GWTYGPVRDD NKRLHPCLVN FHSLPEPERN YNLQMSGETL KTLLALGCH VGMADEKAED NLKKTKLPKT YMMSNGYKPA PLDLSHVRLT PAQTTLVDRL AENGHNVWAR DRVAQGWSYS A VQDIPARR NPRLVPYRLL DEATKRSNRD SLCQAVRTLL GYGYNIEP

UniProtKB: Ryanodine receptor 1

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Macromolecule #2: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 2 / Number of copies: 1 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

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Macromolecule #3: Dantrolene

MacromoleculeName: Dantrolene / type: ligand / ID: 3 / Number of copies: 1 / Formula: U1C
Molecular weightTheoretical: 314.253 Da

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Macromolecule #4: water

MacromoleculeName: water / type: ligand / ID: 4 / Number of copies: 38 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Detector mode: COUNTING / Average electron dose: 58.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.14 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 240758
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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