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- EMDB-52083: Ryanodine receptor1 incomplx with FBKP12 and Nanobody9657 -

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Basic information

Entry
Database: EMDB / ID: EMD-52083
TitleRyanodine receptor1 incomplx with FBKP12 and Nanobody9657
Map data
Sample
  • Complex: Ryanodine receptor 1 complex with nanobody and FKBP12
    • Complex: Ryanodine receptor 1
    • Complex: Nanobody 9657
    • Complex: Peptidyl-prolyl cis-trans isomerase FKBP1B
KeywordsIon channel / Ca2+ / tetramer / TRANSPORT PROTEIN
Biological speciesOryctolagus cuniculus (rabbit) / Vicugna pacos (alpaca)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsLi C / Efremov RG
Funding support Belgium, European Union, 3 items
OrganizationGrant numberCountry
Research Foundation - Flanders (FWO)G0H5916N Belgium
Research Foundation - Flanders (FWO)G054617N Belgium
European Research Council (ERC)726436European Union
CitationJournal: To Be Published
Title: Primed-state RyR1 in 0.05% POPC micelles, in complex with a nanobody and FKBP
Authors: Li C / Efremov RG
History
DepositionNov 14, 2024-
Header (metadata) releaseSep 17, 2025-
Map releaseSep 17, 2025-
UpdateSep 17, 2025-
Current statusSep 17, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_52083.png

Downloads & links

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Map

FileDownload / File: emd_52083.map.gz / Format: CCP4 / Size: 144.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.43 Å/pix.
x 336 pix.
= 479.136 Å		1.43 Å/pix.
x 336 pix.
= 479.136 Å		1.43 Å/pix.
x 336 pix.
= 479.136 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.426 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.3
Minimum - Maximum-2.908613 - 4.8994966
Average (Standard dev.)0.008730712 (±0.10297605)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions336336336
Spacing336336336
CellA=B=C: 479.136 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_52083_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_52083_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_52083_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 1 complex with nanobody and FKBP12

EntireName: Ryanodine receptor 1 complex with nanobody and FKBP12
Components
  • Complex: Ryanodine receptor 1 complex with nanobody and FKBP12
    • Complex: Ryanodine receptor 1
    • Complex: Nanobody 9657
    • Complex: Peptidyl-prolyl cis-trans isomerase FKBP1B

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Supramolecule #1: Ryanodine receptor 1 complex with nanobody and FKBP12

SupramoleculeName: Ryanodine receptor 1 complex with nanobody and FKBP12 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3

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Supramolecule #2: Ryanodine receptor 1

SupramoleculeName: Ryanodine receptor 1 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Oryctolagus cuniculus (rabbit)

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Supramolecule #3: Nanobody 9657

SupramoleculeName: Nanobody 9657 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Vicugna pacos (alpaca)

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Supramolecule #4: Peptidyl-prolyl cis-trans isomerase FKBP1B

SupramoleculeName: Peptidyl-prolyl cis-trans isomerase FKBP1B / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #3
Source (natural)Organism: Oryctolagus cuniculus (rabbit)

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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: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeJEOL CRYO ARM 300
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm
Sample stageSpecimen holder model: JEOL CRYOSPECPORTER

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Image processing

DetailsThe movies were selected after MotionCor correction and CTF refinement with the parameters: total drift less than 30 angstrom and resolution better than 5 angstrom
Particle selectionNumber selected: 333223
Details: Particles were picked by template picking in Cryosparc
CTF correctionSoftware - Name: RELION (ver. 4.1) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

8rrw

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.31) / Number images used: 279776
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final 3D classificationNumber classes: 8 / Software - Name: RELION (ver. 4.1)

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