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- EMDB-50711: Consensus 3D map of the Plastid-encoded RNA polymerase from Sinap... -

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Open data


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Basic information

Entry
Database: EMDB / ID: EMD-50711
TitleConsensus 3D map of the Plastid-encoded RNA polymerase from Sinapis Alba
Map dataConsensus 3D map of PEP
Sample
  • Complex: Plastid-encoded RNA polymerase
KeywordsRNA polymerase Chloroplast Sinapis alba Cryo-EM / TRANSCRIPTION
Biological speciesSinapis alba (white mustard)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsEffantin G / Blanvillain R / Cobessi D
Funding support France, 1 items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-17-CE11-0031 France
CitationJournal: To Be Published
Title: Cryo-EM structure of the Plastid-encoded RNA polymerase from Sinapis alba
Authors: Effantin G / Blanvillain R / Cobessi D
History
DepositionJun 18, 2024-
Header (metadata) releaseJul 2, 2025-
Map releaseJul 2, 2025-
UpdateJul 2, 2025-
Current statusJul 2, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_50711.png

Downloads & links

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Map

FileDownload / File: emd_50711.map.gz / Format: CCP4 / Size: 163.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationConsensus 3D map of PEP
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 350 pix.
= 371. Å		1.06 Å/pix.
x 350 pix.
= 371. Å		1.06 Å/pix.
x 350 pix.
= 371. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.012
Minimum - Maximum-0.018807812 - 0.053427886
Average (Standard dev.)0.00018828028 (±0.0019290418)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions350350350
Spacing350350350
CellA=B=C: 370.99997 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half map 2 for the consensus 3D map of PEP

Fileemd_50711_half_map_1.map
AnnotationHalf map 2 for the consensus 3D map of PEP
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 1 for the consensus 3D map of PEP

Fileemd_50711_half_map_2.map
AnnotationHalf map 1 for the consensus 3D map of PEP
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Plastid-encoded RNA polymerase

EntireName: Plastid-encoded RNA polymerase
Components
  • Complex: Plastid-encoded RNA polymerase

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Supramolecule #1: Plastid-encoded RNA polymerase

SupramoleculeName: Plastid-encoded RNA polymerase / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#19
Source (natural)Organism: Sinapis alba (white mustard)
Molecular weightTheoretical: 1.15 MDa

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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: 7.6
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 51.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.4 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: EMDB MAP
EMDB ID:

14571

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 105796
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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