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- EMDB-18976: Plastid-encoded RNA polymerase (Region 5) -

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Basic information

Entry
Database: EMDB / ID: EMD-18976
TitlePlastid-encoded RNA polymerase (Region 5)
Map dataPlastid-encoded RNA polymerase (Region 5)
Sample
  • Complex: Plastid-encoded RNA polymerase (Region 5)
KeywordsTranscription / chloroplast / RNA polymerase / photosynthesis / GENE REGULATION
Biological speciesSinapis alba (white mustard)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.4 Å
AuthorsWebster MW / Pramanick I / Vergara-Cruces A
Funding support United Kingdom, 4 items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/P013511/1 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/X01102X/1 United Kingdom
Royal SocietyRGS/R2/222157 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)NT33824 United Kingdom
CitationJournal: Cell / Year: 2024
Title: Structure of the plant plastid-encoded RNA polymerase.
Authors: Ángel Vergara-Cruces / Ishika Pramanick / David Pearce / Vinod K Vogirala / Matthew J Byrne / Jason K K Low / Michael W Webster /
Abstract: Chloroplast genes encoding photosynthesis-associated proteins are predominantly transcribed by the plastid-encoded RNA polymerase (PEP). PEP is a multi-subunit complex composed of plastid-encoded ...Chloroplast genes encoding photosynthesis-associated proteins are predominantly transcribed by the plastid-encoded RNA polymerase (PEP). PEP is a multi-subunit complex composed of plastid-encoded subunits similar to bacterial RNA polymerases (RNAPs) stably bound to a set of nuclear-encoded PEP-associated proteins (PAPs). PAPs are essential to PEP activity and chloroplast biogenesis, but their roles are poorly defined. Here, we present cryoelectron microscopy (cryo-EM) structures of native 21-subunit PEP and a PEP transcription elongation complex from white mustard (Sinapis alba). We identify that PAPs encase the core polymerase, forming extensive interactions that likely promote complex assembly and stability. During elongation, PAPs interact with DNA downstream of the transcription bubble and with the nascent mRNA. The models reveal details of the superoxide dismutase, lysine methyltransferase, thioredoxin, and amino acid ligase enzymes that are subunits of PEP. Collectively, these data provide a foundation for the mechanistic understanding of chloroplast transcription and its role in plant growth and adaptation.
History
DepositionNov 25, 2023-
Header (metadata) releaseMar 13, 2024-
Map releaseMar 13, 2024-
UpdateMar 13, 2024-
Current statusMar 13, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_18976.png

Downloads & links

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Map

FileDownload / File: emd_18976.map.gz / Format: CCP4 / Size: 824 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPlastid-encoded RNA polymerase (Region 5)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 600 pix.
= 498.6 Å		0.83 Å/pix.
x 600 pix.
= 498.6 Å		0.83 Å/pix.
x 600 pix.
= 498.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.831 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.03
Minimum - Maximum-0.09489018 - 0.17483854
Average (Standard dev.)-0.000022426675 (±0.002836375)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions600600600
Spacing600600600
CellA=B=C: 498.59998 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Plastid-encoded RNA polymerase (Half map 1 of region 5)

Fileemd_18976_half_map_1.map
AnnotationPlastid-encoded RNA polymerase (Half map 1 of region 5)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Plastid-encoded RNA polymerase (Half map 2 of region 5)

Fileemd_18976_half_map_2.map
AnnotationPlastid-encoded RNA polymerase (Half map 2 of region 5)
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 (Region 5)

EntireName: Plastid-encoded RNA polymerase (Region 5)
Components
  • Complex: Plastid-encoded RNA polymerase (Region 5)

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Supramolecule #1: Plastid-encoded RNA polymerase (Region 5)

SupramoleculeName: Plastid-encoded RNA polymerase (Region 5) / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Sinapis alba (white mustard)

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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 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.4 µm / Nominal defocus min: 0.7000000000000001 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 511166
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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