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- EMDB-50728: Cryo-EM structure of the decameric TraT surface exclusion lipopro... -

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Basic information

Entry
Database: EMDB / ID: EMD-50728
TitleCryo-EM structure of the decameric TraT surface exclusion lipoprotein from Klebsiella pneumoniae (pKpQIL plasmid)
Map data
Sample
  • Complex: Cryo-EM structure of the decameric TraT surface exclusion lipoprotein from Klebsiella pneumoniae (pKpQIL plasmid)
    • Protein or peptide: TraT complement resistance protein
  • Ligand: DIACYL GLYCEROL
Keywordssurface exclusion / decamer / diacylglycerol (DAG) modification / MEMBRANE PROTEIN
Function / homologyEnterobacterial TraT complement resistance / Enterobacterial TraT complement resistance protein / cell outer membrane / TraT complement resistance protein
Function and homology information
Biological speciesKlebsiella pneumoniae (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.47 Å
AuthorsSeddon C / Beis K
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/M011178/1 United Kingdom
CitationJournal: Nat Commun / Year: 2025
Title: Cryo-EM structure and evolutionary history of the conjugation surface exclusion protein TraT.
Authors: Chloe Seddon / Sophia David / Joshua L C Wong / Naito Ishimoto / Shan He / Jonathan Bradshaw / Wen Wen Low / Gad Frankel / Konstantinos Beis /
Abstract: Conjugation plays a major role in dissemination of antimicrobial resistance genes. Following transfer of IncF-like plasmids, recipients become refractory to a second wave of conjugation with the same ...Conjugation plays a major role in dissemination of antimicrobial resistance genes. Following transfer of IncF-like plasmids, recipients become refractory to a second wave of conjugation with the same plasmid via entry (TraS) and surface (TraT) exclusion mechanisms. Here, we show that TraT from the pKpQIL and F plasmids (TraT and TraT) exhibits plasmid surface exclusion specificity. The cryo-EM structures of TraT and TraT reveal that they oligomerise into decameric champagne bottle cork-like structures, which are anchored to the outer membrane via a diacylglycerol and palmitic acid modified α-helical barrel domain. Unexpectedly, we identify chromosomal TraT homologues from multiple Gram-negative phyla which form numerous divergent lineages in a phylogenetic tree of TraT sequences. Plasmid-associated TraT sequences are found in multiple distinct lineages, including two separate clades incorporating TraT from Enterobacteriaceae IncF/F-like and Legionellaceae F-like plasmids. These findings suggest that different plasmid backbones have acquired and co-opted TraT on independent occasions.
History
DepositionJun 21, 2024-
Header (metadata) releaseDec 11, 2024-
Map releaseDec 11, 2024-
UpdateJun 11, 2025-
Current statusJun 11, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_50728.png

Downloads & links

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Map

FileDownload / File: emd_50728.map.gz / Format: CCP4 / Size: 325 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.72 Å/pix.
x 440 pix.
= 316.8 Å		0.72 Å/pix.
x 440 pix.
= 316.8 Å		0.72 Å/pix.
x 440 pix.
= 316.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.72 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.125
Minimum - Maximum-0.3649549 - 1.0389787
Average (Standard dev.)0.002150294 (±0.030304478)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions440440440
Spacing440440440
CellA=B=C: 316.80002 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_50728_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_50728_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 : Cryo-EM structure of the decameric TraT surface exclusion lipopro...

EntireName: Cryo-EM structure of the decameric TraT surface exclusion lipoprotein from Klebsiella pneumoniae (pKpQIL plasmid)
Components
  • Complex: Cryo-EM structure of the decameric TraT surface exclusion lipoprotein from Klebsiella pneumoniae (pKpQIL plasmid)
    • Protein or peptide: TraT complement resistance protein
  • Ligand: DIACYL GLYCEROL

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Supramolecule #1: Cryo-EM structure of the decameric TraT surface exclusion lipopro...

SupramoleculeName: Cryo-EM structure of the decameric TraT surface exclusion lipoprotein from Klebsiella pneumoniae (pKpQIL plasmid)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Klebsiella pneumoniae (bacteria)

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Macromolecule #1: TraT complement resistance protein

MacromoleculeName: TraT complement resistance protein / type: protein_or_peptide / ID: 1
Details: (DGA) corresponds to the posttranslational modification by diacylglycerol (DAG) The last 3 residues GSG are from the expression tag.
Number of copies: 10 / Enantiomer: LEVO
Source (natural)Organism: Klebsiella pneumoniae (bacteria)
Molecular weightTheoretical: 23.989965 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: CSAMGTAIKK RNLEVKTQMS ETIWLEPSNN KTVYLQIKNT SDKDMSGLQA KIASAVTSKG YQVVSNPDTA GYWIQANVLK ADKMDLRES QGWLSRGYEG AVTGAALGAG ITAYNSSSAG ATLGVGLAAG LVGMAADAMV EDVNYTMITD VQIAERTKTQ V QTDNVAVL ...String:
CSAMGTAIKK RNLEVKTQMS ETIWLEPSNN KTVYLQIKNT SDKDMSGLQA KIASAVTSKG YQVVSNPDTA GYWIQANVLK ADKMDLRES QGWLSRGYEG AVTGAALGAG ITAYNSSSAG ATLGVGLAAG LVGMAADAMV EDVNYTMITD VQIAERTKTQ V QTDNVAVL RQGTSGTKVQ TSTETGNQHK YQTRVVSNAN KVNLKFPEAQ PVLEDQLAKS IANILGSG

UniProtKB: TraT complement resistance protein

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Macromolecule #2: DIACYL GLYCEROL

MacromoleculeName: DIACYL GLYCEROL / type: ligand / ID: 2 / Number of copies: 10 / Formula: DGA
Molecular weightTheoretical: 625.018 Da
Chemical component information

ChemComp-DGA:
DIACYL GLYCEROL

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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: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.9 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: 2.47 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 210600
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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Atomic model buiding 1

Initial modelChain - Source name: Other / Chain - Initial model type: in silico model / Details: buccaneer
Output model

PDB-9fsm:
Cryo-EM structure of the decameric TraT surface exclusion lipoprotein from Klebsiella pneumoniae (pKpQIL plasmid)

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