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- EMDB-47469: Cryo-EM map of homodecameric TraT -

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Open data


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Basic information

Entry
Database: EMDB / ID: EMD-47469
TitleCryo-EM map of homodecameric TraT
Map data
Sample
  • Complex: TraT
    • Protein or peptide: TraT complement resistance protein
KeywordsMembrane protein involved in surface exclusion / MEMBRANE PROTEIN
Function / homologyEnterobacterial TraT complement resistance / Enterobacterial TraT complement resistance protein / cell outer membrane / Prokaryotic membrane lipoprotein lipid attachment site profile. / TraT complement resistance protein
Function and homology information
Biological speciesEscherichia coli (E. coli) / Escherichia coli (strain K12) (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.0 Å
AuthorsLundgren CAK / Lea S / Deme J
Funding support1 items
OrganizationGrant numberCountry
Other government
CitationJournal: Commun Biol / Year: 2025
Title: Structure of the conjugation surface exclusion protein TraT.
Authors: Nicolas Chen / Alfredas Bukys / Camilla A K Lundgren / Justin C Deme / Hafez El Sayyed / Achillefs N Kapanidis / Susan M Lea / Ben C Berks /
Abstract: Conjugal transfer of plasmids between bacteria is a major route for the spread of antimicrobial resistance. Many conjugative plasmids encode exclusion systems that inhibit redundant conjugation. In ...Conjugal transfer of plasmids between bacteria is a major route for the spread of antimicrobial resistance. Many conjugative plasmids encode exclusion systems that inhibit redundant conjugation. In incompatibility group F (IncF) plasmids surface exclusion is mediated by the outer membrane protein TraT. Here we report the cryoEM structure of the TraT exclusion protein complex from the canonical F plasmid of Escherichia coli. TraT is a hollow homodecamer shaped like a chef's hat. In contrast to most outer membrane proteins, TraT spans the outer membrane using transmembrane α-helices. We develop a microscopy-based conjugation assay to probe the effects of directed mutagenesis on TraT. Our analysis provides no support for the idea that TraT has specific interactions with partner proteins. Instead, we infer that TraT is most likely to function by physical interference with conjugation. This work provides structural insight into a natural inhibitor of microbial gene transfer.
History
DepositionOct 23, 2024-
Header (metadata) releaseApr 16, 2025-
Map releaseApr 16, 2025-
UpdateDec 10, 2025-
Current statusDec 10, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_47469.png

Downloads & links

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Map

FileDownload / File: emd_47469.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.73 Å/pix.
x 512 pix.
= 374.784 Å		0.73 Å/pix.
x 512 pix.
= 374.784 Å		0.73 Å/pix.
x 512 pix.
= 374.784 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.732 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.22
Minimum - Maximum-0.28418976 - 1.0844675
Average (Standard dev.)0.0006740892 (±0.023735829)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 374.784 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_47469_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: #1

Fileemd_47469_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_47469_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_47469_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 : TraT

EntireName: TraT
Components
  • Complex: TraT
    • Protein or peptide: TraT complement resistance protein

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Supramolecule #1: TraT

SupramoleculeName: TraT / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Escherichia coli (E. coli)

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Macromolecule #1: TraT complement resistance protein

MacromoleculeName: TraT complement resistance protein / type: protein_or_peptide / ID: 1 / Number of copies: 10 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (strain K12) (bacteria) / Strain: K12
Molecular weightTheoretical: 27.668051 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: CGAMSTAIKK RNLEVKTQMS ETIWLEPASE RTVFLQIKNT SDKDMSGLQG KIADAVKAKG YQVVTSPDKA YYWIQANVLK ADKMDLRES QGWLNRGYEG AAVGAALGAG ITGYNSNSAG ATLGVGLAAG LVGMAADAMV EDVNYTMITD VQIAERTKAT V TTDNVAAL ...String:
CGAMSTAIKK RNLEVKTQMS ETIWLEPASE RTVFLQIKNT SDKDMSGLQG KIADAVKAKG YQVVTSPDKA YYWIQANVLK ADKMDLRES QGWLNRGYEG AAVGAALGAG ITGYNSNSAG ATLGVGLAAG LVGMAADAMV EDVNYTMITD VQIAERTKAT V TTDNVAAL RQGTSGAKIQ TSTETGNQHK YQTRVVSNAN KVNLKFEEAK PVLEDQLAKS IANILMDIGI NGTSAWSHPQ FE KGGGSGG GSGGSAWSHP QFEK

UniProtKB: TraT complement resistance protein

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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
Component:
ConcentrationNameFormula
100.0 mMTris-HCl
150.0 mMsodium chlorideNaCl
0.02 %DDM

Details: 100 mM Tris-HCl, 150 mM NaCl, 0.02% DDM
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Pressure: 0.015 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 54.0 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: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 90771
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

3979


Chain - Source name: AlphaFold / Chain - Initial model type: in silico model
RefinementOverall B value: 74.55 / Target criteria: CC
Output model

PDB-9e2v:
Cryo-EM map of homodecameric TraT

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