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- EMDB-54587: Focused Map of the Activation core and TMD parts, Apo-state RyR1 ... -

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Basic information

Entry
Database: EMDB / ID: EMD-54587
TitleFocused Map of the Activation core and TMD parts, Apo-state RyR1 in the native membrane solved by StA
Map dataFiltered according to the local resolution, sharpened with a B-factor of -80.
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: 3.99 Å
AuthorsMikirtumov V
Funding support Germany, 2 items
OrganizationGrant numberCountry
German Research Foundation (DFG)KU3221/3-1 Germany
Helmholtz Association Germany
CitationJournal: To Be Published
Title: Activation of RyR1 in native membranes
Authors: Mikirtumov V / Golusik S / Sprink T / Balyschew N / Yang W / Kotecha A / Kudryashev M
History
DepositionJul 29, 2025-
Header (metadata) releaseAug 12, 2026-
Map releaseAug 12, 2026-
UpdateAug 12, 2026-
Current statusAug 12, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_54587.png

Downloads & links

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Map

FileDownload / File: emd_54587.map.gz / Format: CCP4 / Size: 149.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFiltered according to the local resolution, sharpened with a B-factor of -80.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.97 Å/pix.
x 340 pix.
= 331.16 Å		0.97 Å/pix.
x 340 pix.
= 331.16 Å		0.97 Å/pix.
x 340 pix.
= 331.16 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.974 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0937
Minimum - Maximum-0.29153377 - 0.46944353
Average (Standard dev.)0.0000008763983 (±0.018388491)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions340340340
Spacing340340340
CellA=B=C: 331.16 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_54587_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: #1

Fileemd_54587_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_54587_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_54587_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 : 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: C4 (4 fold cyclic) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.99 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4) / Number subtomograms used: 13726
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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