[English] 日本語
Yorodumi
- EMDB-53548: CryoEM map of the F plasmid relaxosome with TraI in its TE mode. ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-53548
TitleCryoEM map of the F plasmid relaxosome with TraI in its TE mode. ss-27_+8ds+9_+143-R Global 3.77 A Map.
Map dataGlobal refinement map Unsharpened
Sample
  • Complex: Complex of the relaxosome containing oriT DNA, accessory proteins TraY and TraM, host protein IHF and relaxase TraI
    • Complex: Heteroduplex OriT DNA containing the nic site
    • Complex: IHF heterodimer
    • Complex: Train of three TraY proteins
    • Complex: Relaxase/helicase protein TraI
    • Complex: TraM tetramer
KeywordsRelaxosome / Bacterial Conjugation / DNA processing / Relaxase / DNA binding protein
Biological speciesEscherichia coli K-12 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.77 Å
AuthorsWilliams SM / Waksman G
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
Wellcome Trust United Kingdom
CitationJournal: Nat Commun / Year: 2025
Title: Cryo-EM Structure of the relaxosome, a complex essential for bacterial mating and the spread of antibiotic resistance genes.
Authors: Sunanda M Williams / Sandra Raffl / Sabine Kienesberger / Aravindan Ilangovan / Ellen L Zechner / Gabriel Waksman /
Abstract: Bacterial mating, or conjugation, was discovered nearly 80 years ago as a process transferring genes from one bacterial cell (the donor) to another (the recipient). It requires three key multiprotein ...Bacterial mating, or conjugation, was discovered nearly 80 years ago as a process transferring genes from one bacterial cell (the donor) to another (the recipient). It requires three key multiprotein complexes in the donor cell: a DNA-processing machinery called the relaxosome, a double-membrane spanning type 4 secretion system (T4SS), and an extracellular appendage termed pilus. While the near-atomic resolution structures of the T4SS and pilus are already known, that of the relaxosome has not been reported to date. Here, we describe the cryo-EM structure of the fully assembled relaxosome encoded by the paradigm F plasmid in two different states corresponding to distinct functional steps along the DNA processing reaction. By varying the structures of model DNAs we delineate conformational changes required to initiate conjugation. Mutational studies of the various protein-protein and protein-DNA interaction hubs suggest a complex sensitive to trigger signals, that could arise from cell-to-cell contacts with recipient cells.
History
DepositionMay 2, 2025-
Header (metadata) releaseJun 4, 2025-
Map releaseJun 4, 2025-
UpdateJun 4, 2025-
Current statusJun 4, 2025Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_53548.png

Downloads & links

-
Map

FileDownload / File: emd_53548.map.gz / Format: CCP4 / Size: 669.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationGlobal refinement map Unsharpened
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 560 pix.
= 462. Å		0.83 Å/pix.
x 560 pix.
= 462. Å		0.83 Å/pix.
x 560 pix.
= 462. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.825 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.15
Minimum - Maximum-0.23922163 - 1.1041424
Average (Standard dev.)0.0009096063 (±0.024117462)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions560560560
Spacing560560560
CellA=B=C: 462.0 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: Global refinement map - Half-B

Fileemd_53548_half_map_1.map
AnnotationGlobal refinement map - Half-B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Global refinement map - Half-A

Fileemd_53548_half_map_2.map
AnnotationGlobal refinement map - Half-A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Complex of the relaxosome containing oriT DNA, accessory proteins...

EntireName: Complex of the relaxosome containing oriT DNA, accessory proteins TraY and TraM, host protein IHF and relaxase TraI
Components
  • Complex: Complex of the relaxosome containing oriT DNA, accessory proteins TraY and TraM, host protein IHF and relaxase TraI
    • Complex: Heteroduplex OriT DNA containing the nic site
    • Complex: IHF heterodimer
    • Complex: Train of three TraY proteins
    • Complex: Relaxase/helicase protein TraI
    • Complex: TraM tetramer

-
Supramolecule #1: Complex of the relaxosome containing oriT DNA, accessory proteins...

SupramoleculeName: Complex of the relaxosome containing oriT DNA, accessory proteins TraY and TraM, host protein IHF and relaxase TraI
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#6
Source (natural)Organism: Escherichia coli K-12 (bacteria)

-
Supramolecule #2: Heteroduplex OriT DNA containing the nic site

SupramoleculeName: Heteroduplex OriT DNA containing the nic site / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#2
Details: Prepared by annealing of chemically synthesised oligos
Source (natural)Organism: Escherichia coli K-12 (bacteria)

-
Supramolecule #3: IHF heterodimer

SupramoleculeName: IHF heterodimer / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #3-#4
Source (natural)Organism: Escherichia coli K-12 (bacteria)

-
Supramolecule #4: Train of three TraY proteins

SupramoleculeName: Train of three TraY proteins / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #5
Source (natural)Organism: Escherichia coli K-12 (bacteria)

-
Supramolecule #5: Relaxase/helicase protein TraI

SupramoleculeName: Relaxase/helicase protein TraI / type: complex / ID: 5 / Parent: 1 / Macromolecule list: #6
Source (natural)Organism: Escherichia coli K-12 (bacteria)

-
Supramolecule #6: TraM tetramer

SupramoleculeName: TraM tetramer / type: complex / ID: 6 / Parent: 1
Source (natural)Organism: Escherichia coli K-12 (bacteria)

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5 / Details: 20 mM Hepes pH 7.5, 100 mM NaCl
GridModel: UltrAuFoil R2/2 / Material: GOLD / Mesh: 200 / Support film - Material: GRAPHENE OXIDE / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV
DetailsThe complex after assembly and gel filtration was subjected to glutaraldehyde crosslinking.

-
Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.4 e/Å2
Details: Movies were collected in counting mode fractionated over 50 frames
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: OTHER / Nominal defocus max: 2.7 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 105000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 3830425
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER / Details: CryoSPARC ab-initio
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.77 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 155077
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Details: CryoSPARC ab-initio
Final angle assignmentType: MAXIMUM LIKELIHOOD / Details: Homogeneous refinement
FSC plot (resolution estimation)

-
Atomic model buiding 1

RefinementProtocol: RIGID BODY FIT

+
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