[English] 日本語
Yorodumi
- EMDB-51258: RNAP-TopoI complex on duplex scaffold - focused map (RNAP beta pr... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-51258
TitleRNAP-TopoI complex on duplex scaffold - focused map (RNAP beta protrusion and lobe)
Map dataRNAP-TopoI complex on duplex scaffold focused refinement (RNAP beta protrusion & lobe) - deepemhanced map
Sample
  • Complex: RNAP-TopoI complex on duplex scaffold
    • Complex: DNA-directed RNA polymerase elongation complex
    • Complex: DNA topoisomerase 1
KeywordsRNA polymerase / topoisomerase / DNA topology / TRANSCRIPTION
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsVidmar V / Weixlbaumer A / Lamour V
Funding support France, 2 items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-21-CE11-0040-01 France
Agence Nationale de la Recherche (ANR)ANR-10-INBS-05 France
CitationJournal: Nat Struct Mol Biol / Year: 2025
Title: DNA topoisomerase I acts as supercoiling sensor for bacterial transcription elongation.
Authors: Vita Vidmar / Céline Borde / Lisa Bruno / Nataliya Miropolskaya / Maria Takacs / Claire Batisse / Charlotte Saint-André / Chengjin Zhu / Olivier Espéli / Valérie Lamour / Albert Weixlbaumer /
Abstract: During transcription, RNA polymerase (RNAP) continuously unwinds and rewinds DNA, generating negative and positive supercoils upstream and downstream, respectively. Using single-particle cryo-EM, we ...During transcription, RNA polymerase (RNAP) continuously unwinds and rewinds DNA, generating negative and positive supercoils upstream and downstream, respectively. Using single-particle cryo-EM, we elucidated how bacterial RNAP and DNA topoisomerase I (TopoI), which relaxes negative supercoils, operate in close spatial proximity. TopoI binds to relaxed DNA upstream of RNAP, and this involves a conformational switch in the TopoI functional domains. This suggests that TopoI exerts a sensing role before the formation of negative supercoils. On DNA substrates mimicking negatively supercoiled DNA, TopoI threads one strand into the active site for cleavage and binds the complementary strand with an auxiliary domain. Transcriptomic and phenotypic analyses suggest that mutations affecting conformational changes in TopoI impact gene expression and operon polarity in bacteria. In summary, we propose a comprehensive model for DNA relaxation in the proximity of active bacterial transcription.
History
DepositionAug 5, 2024-
Header (metadata) releaseNov 5, 2025-
Map releaseNov 5, 2025-
UpdateDec 17, 2025-
Current statusDec 17, 2025Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_51258.png

Downloads & links

-
Map

FileDownload / File: emd_51258.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationRNAP-TopoI complex on duplex scaffold focused refinement (RNAP beta protrusion & lobe) - deepemhanced map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 360 pix.
= 302.04 Å		0.84 Å/pix.
x 360 pix.
= 302.04 Å		0.84 Å/pix.
x 360 pix.
= 302.04 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.839 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0242
Minimum - Maximum-0.04881287 - 1.4829023
Average (Standard dev.)0.0017011849 (±0.021908069)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 302.04 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_51258_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Mask #2

Fileemd_51258_msk_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: RNAP-TopoI complex on duplex scaffold focused refinement (RNAP...

Fileemd_51258_additional_1.map
AnnotationRNAP-TopoI complex on duplex scaffold focused refinement (RNAP beta protrusion & lobe) - unsharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: RNAP-TopoI complex on duplex scaffold focused refinement (RNAP...

Fileemd_51258_half_map_1.map
AnnotationRNAP-TopoI complex on duplex scaffold focused refinement (RNAP beta protrusion & lobe) - halfmap A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: RNAP-TopoI complex on duplex scaffold focused refinement (RNAP...

Fileemd_51258_half_map_2.map
AnnotationRNAP-TopoI complex on duplex scaffold focused refinement (RNAP beta protrusion & lobe) - halfmap B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : RNAP-TopoI complex on duplex scaffold

EntireName: RNAP-TopoI complex on duplex scaffold
Components
  • Complex: RNAP-TopoI complex on duplex scaffold
    • Complex: DNA-directed RNA polymerase elongation complex
    • Complex: DNA topoisomerase 1

-
Supramolecule #1: RNAP-TopoI complex on duplex scaffold

SupramoleculeName: RNAP-TopoI complex on duplex scaffold / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#9
Molecular weightTheoretical: 100 KDa

-
Supramolecule #2: DNA-directed RNA polymerase elongation complex

SupramoleculeName: DNA-directed RNA polymerase elongation complex / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#5, #7-#9
Source (natural)Organism: Escherichia coli (E. coli)

-
Supramolecule #3: DNA topoisomerase 1

SupramoleculeName: DNA topoisomerase 1 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #6
Source (natural)Organism: Escherichia coli (E. coli)

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration10 mg/mL
BufferpH: 7.5
Component:
ConcentrationName
10.0 mMHEPES/KOH
150.0 mMpotassium acetate
5.0 mMmagnesium acetate
0.01 mMzinc chloride
2.0 mMDTT
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY / Support film - Film thickness: 50 / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 35 sec. / Pretreatment - Atmosphere: OTHER
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 283 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 56.6 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.8 µm
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 113760
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial model
PDB IDChain

6alh

source_name: PDB, initial_model_type: experimental model

4rul

source_name: PDB, initial_model_type: experimental model
DetailsInitial rigid body fit was done in UCSF Chimera, followed by flexible fitting in Isolde. The entire model was further refined in Phenix and Coot.
RefinementSpace: REAL

+
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