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- EMDB-52933: Consensus map of bacterial transcription intermediate complex med... -

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Basic information

Entry
Database: EMDB / ID: EMD-52933
TitleConsensus map of bacterial transcription intermediate complex mediated by activator PspF containing nifH promoter DNA containing mismatch from -11 to -8 - conformation 6
Map data
Sample
  • Complex: Subtracted refinement map of conformation 1 of PspF(1-275)-sigma54 bound to nifH DNA (-28 to +35) containing mismatch from -11 to -8.
Keywordssigma factor / transcription / complex / AAA+ / DNA-binding protein
Biological speciesEscherichia coli K-12 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 7.2 Å
AuthorsGao F / Zhang X
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC) United Kingdom
CitationJournal: To Be Published
Title: Subunit specialisation in AAA+ proteins and substrate unfolding during transcription complex remodelling
Authors: Gao F / Ye F / Buck M / Zhang X
History
DepositionFeb 26, 2025-
Header (metadata) releaseApr 2, 2025-
Map releaseApr 2, 2025-
UpdateApr 2, 2025-
Current statusApr 2, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_52933.png

Downloads & links

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Map

FileDownload / File: emd_52933.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 280 pix.
= 308. Å		1.1 Å/pix.
x 280 pix.
= 308. Å		1.1 Å/pix.
x 280 pix.
= 308. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.021
Minimum - Maximum-0.01435149 - 0.07582354
Average (Standard dev.)0.0008621548 (±0.0045507196)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 308.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_52933_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_52933_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 : Subtracted refinement map of conformation 1 of PspF(1-275)-sigma5...

EntireName: Subtracted refinement map of conformation 1 of PspF(1-275)-sigma54 bound to nifH DNA (-28 to +35) containing mismatch from -11 to -8.
Components
  • Complex: Subtracted refinement map of conformation 1 of PspF(1-275)-sigma54 bound to nifH DNA (-28 to +35) containing mismatch from -11 to -8.

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Supramolecule #1: Subtracted refinement map of conformation 1 of PspF(1-275)-sigma5...

SupramoleculeName: Subtracted refinement map of conformation 1 of PspF(1-275)-sigma54 bound to nifH DNA (-28 to +35) containing mismatch from -11 to -8.
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#12
Source (natural)Organism: Escherichia coli K-12 (bacteria)

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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: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (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: 3.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: EMDB MAP
EMDB ID:

14171

Final reconstructionAlgorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 7.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 22724
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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