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- EMDB-42652: Constituent EM map: Focused refinement RY3&4 of the Structure of ... -

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Basic information

Entry
Database: EMDB / ID: EMD-42652
TitleConstituent EM map: Focused refinement RY3&4 of the Structure of human RyR2-S2808D in the subprimed state in the presence of H2O2/NOC-12/GSH
Map dataConstituent EM map: Focused refinement RY3&4 of the Structure of human RyR2-S2808D in the subprimed state in the presence of H2O2/NOC-12/GSH
Sample
  • Complex: Complex of RyR2-S2808D and Calstabin-2 in the presence of H2O2/NOC-12/GSH
    • Complex: Ryanodine Receptor 2
    • Complex: Peptidyl- cis-trans isomerase FKBP1B
Keywordscalcium channel / MEMBRANE PROTEIN
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.72 Å
AuthorsMiotto MC / 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: To Be Published
Title: Structural basis for ryanodine receptor type 2 leak in heart failure and arrhythmogenic disorders
Authors: Miotto MC
History
DepositionNov 6, 2023-
Header (metadata) releaseNov 13, 2024-
Map releaseNov 13, 2024-
UpdateNov 13, 2024-
Current statusNov 13, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_42652.png

Downloads & links

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Map

FileDownload / File: emd_42652.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationConstituent EM map: Focused refinement RY3&4 of the Structure of human RyR2-S2808D in the subprimed state in the presence of H2O2/NOC-12/GSH
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: 0.16
Minimum - Maximum-0.12742265 - 0.30730382
Average (Standard dev.)0.0021078682 (±0.01088619)
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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Half map: halfmap A

Fileemd_42652_half_map_1.map
Annotationhalfmap A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: halfmap B

Fileemd_42652_half_map_2.map
Annotationhalfmap B
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 RyR2-S2808D and Calstabin-2 in the presence of H2O2/NO...

EntireName: Complex of RyR2-S2808D and Calstabin-2 in the presence of H2O2/NOC-12/GSH
Components
  • Complex: Complex of RyR2-S2808D and Calstabin-2 in the presence of H2O2/NOC-12/GSH
    • Complex: Ryanodine Receptor 2
    • Complex: Peptidyl- cis-trans isomerase FKBP1B

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Supramolecule #1: Complex of RyR2-S2808D and Calstabin-2 in the presence of H2O2/NO...

SupramoleculeName: Complex of RyR2-S2808D and Calstabin-2 in the presence of H2O2/NOC-12/GSH
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2

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Supramolecule #2: Ryanodine Receptor 2

SupramoleculeName: Ryanodine Receptor 2 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #3: Peptidyl- cis-trans isomerase FKBP1B

SupramoleculeName: Peptidyl- cis-trans isomerase FKBP1B / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Homo sapiens (human)

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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

Concentration2.5 mg/mL
BufferpH: 7.4
Component:
ConcentrationFormulaName
230.0 mMNaClsodium chloride
10.0 mMHEPESHEPES
0.4 %CHAPSCHAPS
1.0 mMEGTAEGTA
0.5 mMTCEPtris(2-carboxyethyl)phosphine
0.001 %DOPCDOPC
10.0 mMATPATP
0.3 mMH2O2hydrogen peroxide
1.0 mMNOC-12NOC-12
1.0 mMGSHglutathione

Details: 30 minute incubation with H2O2/NOC-12/GSH was stopped by flash freezing (vitrobot)
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN 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: 1.2 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

Startup modelType of model: INSILICO MODEL / In silico model: CryoSPARC ab initio
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.72 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 41517
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD

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Atomic model buiding 1

Initial modelPDB ID:

7ua5


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

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