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- EMDB-47406: Structure of RyR1 in the open state in the presence of oxopyricid... -

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Basic information

Entry
Database: EMDB / ID: EMD-47406
TitleStructure of RyR1 in the open state in the presence of oxopyricid, focused refinement
Map dataStructure of RyR1 in the open state in the presence of oxopyricid - focused refinement
Sample
  • Complex: Complex of RyR1 and Calstabin-1
    • Complex: Ryanodine Receptor 1
    • Complex: Calstabin-1
Keywordscalcium channel / MEMBRANE PROTEIN / sarcoplasmic reticulum
Biological speciesOryctolagus cuniculus (rabbit)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.65 Å
AuthorsMiotto MC / Marks AR
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Targeting Ryanodine Receptors with Allopurinol and Xanthine Derivatives for the Treatment of Cardiac and Musculoskeletal Weakness Disorders
Authors: Miotto MC
History
DepositionOct 21, 2024-
Header (metadata) releaseOct 30, 2024-
Map releaseOct 30, 2024-
UpdateOct 30, 2024-
Current statusOct 30, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_47406.png

Downloads & links

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Map

FileDownload / File: emd_47406.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationStructure of RyR1 in the open state in the presence of oxopyricid - focused refinement
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 512 pix.
= 423.68 Å		0.83 Å/pix.
x 512 pix.
= 423.68 Å		0.83 Å/pix.
x 512 pix.
= 423.68 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.8275 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.15
Minimum - Maximum-0.36313444 - 0.79541314
Average (Standard dev.)0.000053961838 (±0.01783039)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 423.68 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_47406_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_47406_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 and Calstabin-1

EntireName: Complex of RyR1 and Calstabin-1
Components
  • Complex: Complex of RyR1 and Calstabin-1
    • Complex: Ryanodine Receptor 1
    • Complex: Calstabin-1

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Supramolecule #1: Complex of RyR1 and Calstabin-1

SupramoleculeName: Complex of RyR1 and Calstabin-1 / type: complex / ID: 1 / Parent: 0

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Supramolecule #2: Ryanodine Receptor 1

SupramoleculeName: Ryanodine Receptor 1 / type: complex / ID: 2 / Parent: 1
Source (natural)Organism: Oryctolagus cuniculus (rabbit)

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Supramolecule #3: Calstabin-1

SupramoleculeName: Calstabin-1 / type: complex / ID: 3 / Parent: 1 / Details: Peptidyl- cis-trans isomerase FKBP1A
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

Concentration10 mg/mL
BufferpH: 7.4
Component:
ConcentrationFormulaName
10.0 mMHEPESHEPES
500.0 mMNaClsodium chloride
0.2 %CHAPSCHAPS
1.0 mMEGTAEGTA
0.5 mMTCEPtris(2-carboxyethyl)phosphine
0.01 %DOPCDOPC
10.0 mMATPATP
1.6 mMCaCl2calcium chloride

Details: 2 mM oxopyricid was added to the final sample from a 20 mM stock solution in buffer.
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
TemperatureMin: 80.0 K / Max: 100.0 K
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / 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: 1.5 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

Startup modelType of model: INSILICO MODEL / In silico model: CryoSPARC ab initio
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.65 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 133232
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD

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Atomic model buiding 1

Initial modelPDB ID:

7tzc


Chain - Source name: PDB / Chain - Initial model type: experimental model

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