[English] 日本語
Yorodumi
- EMDB-51775: Focused map #1 of the cryo-EM structure of Vibrio cholerae RNA po... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-51775
TitleFocused map #1 of the cryo-EM structure of Vibrio cholerae RNA polymerase Transcription Activation Complex with ToxR transcription factor and bound to an ompU promoter DNA fragment
Map dataTAC_ompU Multibody Refinement body 1 Map B Sharpened.
Sample
  • Complex: Virulent transcription complex #3
    • Complex: DNA-directed RNA polymerase
    • Complex: Double stranded DNA
KeywordsRNA polymerase / Open promoter complex / ompU / Vibrio cholerae / TRANSCRIPTION
Biological speciesVibrio cholerae O395 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsAlcaide-Jimenez A / Baudin F / Canals A / Machon C / Murciano B / Fabrega-Ferrer M / Bantysh O / Perez-Luque R / Krukonis ES / Muller CW / Coll M
Funding support Spain, 2 items
OrganizationGrant numberCountry
Ministerio de Ciencia e Innovacion (MCIN)PID2020-12141GB-100 Spain
Generalitat de Catalunya2021SGR00423 Spain
CitationJournal: Science Advances / Year: 2025
Title: Structures of Vibrio cholerae transcription complexes reveal how ToxR and TcpP recruit the RNA polymerase and activate virulence genes
Authors: Alcaide-Jimenez A / Canals A / Baudin F / Machon C / Fabrega-Ferrer M / Bantysh O / Perez-Luque R / Murciano B / Mohammad AA / Rowse MJ / Ferracciolo JM / Krukonis ES / Muller CW / Coll M
History
DepositionOct 10, 2024-
Header (metadata) releaseDec 17, 2025-
Map releaseDec 17, 2025-
UpdateDec 17, 2025-
Current statusDec 17, 2025Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_51775.png

Downloads & links

-
Map

FileDownload / File: emd_51775.map.gz / Format: CCP4 / Size: 347.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationTAC_ompU Multibody Refinement body 1 Map B Sharpened.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 450 pix.
= 369.9 Å		0.82 Å/pix.
x 450 pix.
= 369.9 Å		0.82 Å/pix.
x 450 pix.
= 369.9 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.822 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.116
Minimum - Maximum-0.023176694 - 1.7900846
Average (Standard dev.)0.0011321997 (±0.022363206)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions450450450
Spacing450450450
CellA=B=C: 369.90002 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Additional map: TAC ompU Multibody Refinement body 1 Map B.

Fileemd_51775_additional_1.map
AnnotationTAC_ompU Multibody Refinement body 1 Map B.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: TAC ompU Multibody Refinement unsharpened half map 1.

Fileemd_51775_half_map_1.map
AnnotationTAC_ompU Multibody Refinement unsharpened half map 1.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: TAC ompU Multibody Refinement unsharpened half map 2.

Fileemd_51775_half_map_2.map
AnnotationTAC_ompU Multibody Refinement unsharpened half map 2.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Virulent transcription complex #3

EntireName: Virulent transcription complex #3
Components
  • Complex: Virulent transcription complex #3
    • Complex: DNA-directed RNA polymerase
    • Complex: Double stranded DNA

-
Supramolecule #1: Virulent transcription complex #3

SupramoleculeName: Virulent transcription complex #3 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#8

-
Supramolecule #2: DNA-directed RNA polymerase

SupramoleculeName: DNA-directed RNA polymerase / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#6
Source (natural)Organism: Vibrio cholerae O395 (bacteria)

-
Supramolecule #3: Double stranded DNA

SupramoleculeName: Double stranded DNA / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #7-#8
Source (natural)Organism: Vibrio cholerae O395 (bacteria)

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.4 mg/mL
BufferpH: 8
Details: 10 mM HEPES pH 8.0, 500 mM NaCl, 1 mM DTT and 0.1 mM EDTA
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 51.24 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: 0.7000000000000001 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 158389
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more