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- EMDB-54596: RyR1-RyR1 dimer map, Apo-state RyR1 in the native membrane solved... -

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Basic information

Entry
Database: EMDB / ID: EMD-54596
TitleRyR1-RyR1 dimer map, Apo-state RyR1 in the native membrane solved by StA
Map data
Sample
  • Organelle or cellular component: Ryanodine receptor type 1 in complex with FKBP12 in the sarcoplasmic reticulum membrane
Keywordsryanodine receptor type 1 / ryr1 / skeletal muscle / sarcoplasmic reticulum / SR / native membrane / MEMBRANE PROTEIN
Biological speciesOryctolagus cuniculus (rabbit)
Methodsubtomogram averaging / cryo EM / Resolution: 25.97 Å
AuthorsMikirtumov V
Funding support Germany, 2 items
OrganizationGrant numberCountry
German Research Foundation (DFG)KU3221/3-1 Germany
Helmholtz Association Germany
CitationJournal: Nat Commun / Year: 2026
Title: Ligand-induced activation of RyR1 in native membranes.
Authors: Vasilii Mikirtumov / Sabrina Golusik / Ruifeng Huo / Thiemo Sprink / Nikita Balyschew / Wen Yang / Christoph Diebolder / Shuguang Yuan / Abhay Kotecha / Mikhail Kudryashev /
Abstract: Synchronized calcium release through arrays of the ryanodine receptor RyR1, fundamental to skeletal muscle excitation-contraction coupling, is achieved through the mechanical interaction of RyR1s and ...Synchronized calcium release through arrays of the ryanodine receptor RyR1, fundamental to skeletal muscle excitation-contraction coupling, is achieved through the mechanical interaction of RyR1s and voltage-sensing receptors DHPR that activate RyR1s in response to action potentials. The calcium release is enhanced through "coupled gating", when the activation of one channel promotes the opening of its neighbours. Here, we determine high-resolution structures of RyR1 in native sarcoplasmic reticulum membranes by cryo-EM/ET, capturing the conformations along the activation pathway and corner-to-corner interfaces between adjacent RyR1 receptors. Compared with purified RyR1s, receptors in native membranes follow an activation pathway with reduced cytosolic-shell tilt and greater consecutive in-plane rotation. Activation-induced rotation remodels the inter-receptor interface, lowering the energy barrier to the cooperative opening of the receptor cluster. Our analysis demonstrates how the native membrane receptor lattice influences ion channel cluster dynamics and provides a mechanistic framework for understanding calcium signaling in muscle.
History
DepositionJul 29, 2025-
Header (metadata) releaseAug 12, 2026-
Map releaseAug 12, 2026-
UpdateOct 7, 2026-
Current statusOct 7, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_54596.png

Downloads & links

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Map

FileDownload / File: emd_54596.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
3.9 Å/pix.
x 200 pix.
= 779.2 Å		3.9 Å/pix.
x 200 pix.
= 779.2 Å		3.9 Å/pix.
x 200 pix.
= 779.2 Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 3.896 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0396
Minimum - Maximum-0.1930247 - 0.23219442
Average (Standard dev.)0.0022204844 (±0.028382206)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 779.19995 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_54596_msk_1.map
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AxesZYX

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Half map: #1

Fileemd_54596_half_map_1.map
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Half map: #2

Fileemd_54596_half_map_2.map
Projections & Slices
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Sample components

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Entire : Ryanodine receptor type 1 in complex with FKBP12 in the sarcoplas...

EntireName: Ryanodine receptor type 1 in complex with FKBP12 in the sarcoplasmic reticulum membrane
Components
  • Organelle or cellular component: Ryanodine receptor type 1 in complex with FKBP12 in the sarcoplasmic reticulum membrane

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Supramolecule #1: Ryanodine receptor type 1 in complex with FKBP12 in the sarcoplas...

SupramoleculeName: Ryanodine receptor type 1 in complex with FKBP12 in the sarcoplasmic reticulum membrane
type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Details: Sarcoplasmic reticulum membrane vesicles purified from the native skeletal muscle tissue
Source (natural)Organism: Oryctolagus cuniculus (rabbit) / Organ: hind leg and back / Tissue: skeletal muscle / Organelle: sarcoplasmic reticulum
Molecular weightTheoretical: 2.2 MDa

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation stateparticle

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Sample preparation

Concentration29.5 mg/mL
BufferpH: 7.1
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: TFS Selectris X / Energy filter - Slit width: 10 eV
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Digitization - Dimensions - Width: 8192 pixel / Digitization - Dimensions - Height: 8192 pixel / Number real images: 1 / Average exposure time: 1.88 sec. / Average electron dose: 4.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Calibrated defocus max: 3.8000000000000003 µm / Calibrated defocus min: 1.8 µm / Calibrated magnification: 64000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 5.0 µm / Nominal defocus min: 3.0 µm / Nominal magnification: 64000
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

Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 25.97 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4) / Number subtomograms used: 222
ExtractionNumber tomograms: 194 / Number images used: 44333 / Reference model: EMD-17272 / Method: Dynamo-GPU TomoBEAR Template Matching / Software - Name: Dynamo
CTF correctionSoftware: (Name: Gctf, IMOD, RELION (ver. 4)) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Final 3D classificationNumber classes: 3 / Software - Name: RELION (ver. 4)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

7tzc


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT

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