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- EMDB-61498: Cryo-EM structure of Mycobacterium tuberculosis transcription act... -

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Basic information

Entry
Database: EMDB / ID: EMD-61498
TitleCryo-EM structure of Mycobacterium tuberculosis transcription activation complex with six PhoP molecules focusing on PhoP region
Map data
Sample
  • Complex: Mycobacterium tuberculosis transcription activation complex with six PhoP molecules focusing on PhoP region
Keywordsbacterial RNA polymerase / GENE REGULATION
Biological speciesMycobacterium tuberculosis (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 5.9 Å
AuthorsLin W / Feng Y
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Nat Commun / Year: 2025
Title: Structural insights into transcription regulation of the global OmpR/PhoB family regulator PhoP from Mycobacterium tuberculosis
Authors: Shi J / Feng Z / Song Q / Wen A / Liu T / Xu L / Ye Z / Xu S / Gao F / Xiao L / Zhu J / Das K / Zhao G / Li J / Feng Y / Lin W
History
DepositionSep 11, 2024-
Header (metadata) releaseSep 17, 2025-
Map releaseSep 17, 2025-
UpdateApr 1, 2026-
Current statusApr 1, 2026Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_61498.png

Downloads & links

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Map

FileDownload / File: emd_61498.map.gz / Format: CCP4 / Size: 824 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.6 Å/pix.
x 600 pix.
= 360. Å		0.6 Å/pix.
x 600 pix.
= 360. Å		0.6 Å/pix.
x 600 pix.
= 360. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.6 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.16817166 - 0.12783189
Average (Standard dev.)-0.00061802834 (±0.0027111622)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions600600600
Spacing600600600
CellA=B=C: 360.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_61498_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_61498_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 : Mycobacterium tuberculosis transcription activation complex with ...

EntireName: Mycobacterium tuberculosis transcription activation complex with six PhoP molecules focusing on PhoP region
Components
  • Complex: Mycobacterium tuberculosis transcription activation complex with six PhoP molecules focusing on PhoP region

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Supramolecule #1: Mycobacterium tuberculosis transcription activation complex with ...

SupramoleculeName: Mycobacterium tuberculosis transcription activation complex with six PhoP molecules focusing on PhoP region
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#8
Source (natural)Organism: Mycobacterium tuberculosis (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: 7.9
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: 52.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6vvy

Final reconstructionResolution.type: BY AUTHOR / Resolution: 5.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 82141
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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