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- EMDB-73154: Constituent EM map: Focused refinement on NTD+SPRY+Calstabin-1 of... -

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Basic information

Entry
Database: EMDB / ID: EMD-73154
TitleConstituent EM map: Focused refinement on NTD+SPRY+Calstabin-1 of mouse RyR1 (Ca2+/CFF/ATP dataset; closed pore)
Map dataConstituent EM map: Focused refinement on NTD/SPRY/Calstabin-1 of mouse RyR1 (Ca/CFF/ATP dataset; closed pore)
Sample
  • Complex: Complex of RyR1 with Calstabin-1 (Ca2+/CFF/ATP condition)
KeywordsCalcium / Ion Channel / Membrane Protein
Biological speciesMus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.2 Å
AuthorsWeninger G / Marks AR
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)R01HL145473 United States
CitationJournal: J Clin Invest / Year: 2025
Title: Structural basis for simvastatin-induced skeletal muscle weakness associated with type 1 ryanodine receptor T4709M mutation.
Authors: Gunnar Weninger / Haikel Dridi / Steven Reiken / Qi Yuan / Nan Zhao / Linda Groom / Jennifer Leigh / Yang Liu / Carl Tchagou / Jiayi Kang / Alexander Chang / Estefania Luna-Figueroa / Marco ...Authors: Gunnar Weninger / Haikel Dridi / Steven Reiken / Qi Yuan / Nan Zhao / Linda Groom / Jennifer Leigh / Yang Liu / Carl Tchagou / Jiayi Kang / Alexander Chang / Estefania Luna-Figueroa / Marco C Miotto / Anetta Wronska / Robert T Dirksen / Andrew R Marks /
Abstract: Statins lower cholesterol, reducing the risk of heart disease, and are among the most frequently prescribed drugs. Approximately 10% of individuals develop statin-associated muscle symptoms (SAMS; ...Statins lower cholesterol, reducing the risk of heart disease, and are among the most frequently prescribed drugs. Approximately 10% of individuals develop statin-associated muscle symptoms (SAMS; myalgias, rhabdomyolysis, and muscle weakness), often rendering them statin intolerant. The mechanism underlying SAMS remains poorly understood. Patients with mutations in the skeletal muscle ryanodine receptor 1 (RyR1)/calcium release channel can be particularly intolerant of statins. High-resolution structures revealed simvastatin binding sites in the pore region of RyR1. Simvastatin stabilized the open conformation of the pore and activated the RyR1 channel. In a mouse expressing a mutant RyR1-T4709M found in a patient with profound statin intolerance, simvastatin caused muscle weakness associated with leaky RyR1 channels. Cotreatment with a Rycal drug that stabilizes the channel closed state prevented simvastatin-induced muscle weakness. Thus, statin binding to RyR1 can cause SAMS, and patients with RyR1 mutations may represent a high-risk group for statin intolerance.
History
DepositionOct 10, 2025-
Header (metadata) releaseDec 31, 2025-
Map releaseDec 31, 2025-
UpdateDec 31, 2025-
Current statusDec 31, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_73154.png

Downloads & links

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Map

FileDownload / File: emd_73154.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationConstituent EM map: Focused refinement on NTD/SPRY/Calstabin-1 of mouse RyR1 (Ca/CFF/ATP dataset; closed pore)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 512 pix.
= 424.96 Å		0.83 Å/pix.
x 512 pix.
= 424.96 Å		0.83 Å/pix.
x 512 pix.
= 424.96 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: 0.15
Minimum - Maximum-0.21067636 - 0.608279
Average (Standard dev.)0.0017474317 (±0.01576145)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 424.96 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: map sharp

Fileemd_73154_additional_1.map
Annotationmap_sharp
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_73154_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_73154_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Complex of RyR1 with Calstabin-1 (Ca2+/CFF/ATP condition)

EntireName: Complex of RyR1 with Calstabin-1 (Ca2+/CFF/ATP condition)
Components
  • Complex: Complex of RyR1 with Calstabin-1 (Ca2+/CFF/ATP condition)

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Supramolecule #1: Complex of RyR1 with Calstabin-1 (Ca2+/CFF/ATP condition)

SupramoleculeName: Complex of RyR1 with Calstabin-1 (Ca2+/CFF/ATP condition)
type: complex / ID: 1 / Parent: 0 / Details: 0.03 mM free Ca2+; 5 mM Caffeine; 10 mM ATP
Source (natural)Organism: Mus musculus (house mouse)

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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

Concentration8.5 mg/mL
BufferpH: 7.4
Component:
ConcentrationNameFormula
10.0 mmol/LHEPES
400.0 mmol/Lsodium chlorideNaCl
1.0 mmol/LEGTA
0.25 %CHAPS
0.01 %DOPC
0.5 mmol/LTCEP
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 4695 / Average electron dose: 58.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.2 µm / Nominal defocus min: 0.5 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL / In silico model: CryoSPARC ab initio
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 897756
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC / Details: CryoSPARC branch-and-bound
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC / Details: CryoSPARC branch-and-bound
FSC plot (resolution estimation)

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