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- PDB-9fs5: Cryo-EM structure of the decameric TraT surface exclusion lipopro... -

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Basic information

Entry
Database: PDB / ID: 9fs5
TitleCryo-EM structure of the decameric TraT surface exclusion lipoprotein from Escherichia coli (F plasmid)
ComponentsTraT complement resistance protein
KeywordsMEMBRANE PROTEIN / surface exclusion / decamer / diacylglycerol (DAG) modification
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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.66 Å
AuthorsSeddon, C. / Beis, K.
Funding support United Kingdom, 1items
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 20, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 11, 2024Provider: repository / Type: Initial release
Revision 1.1Jun 11, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TraT complement resistance protein
B: TraT complement resistance protein
C: TraT complement resistance protein
D: TraT complement resistance protein
E: TraT complement resistance protein
F: TraT complement resistance protein
G: TraT complement resistance protein
H: TraT complement resistance protein
I: TraT complement resistance protein
J: TraT complement resistance protein


Theoretical massNumber of molelcules
Total (without water)239,79110
Polymers239,79110
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, reconstruction showed a 10fold symmetry, gel filtration, elution volume corresponded to decamer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
TraT complement resistance protein


Mass: 23979.094 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli)
Gene: traT, traT_2, ACU57_00410, DTL43_23980, DU321_18605, E6D34_19660, EN85_003940, ETECE562_05006, EWK56_24090, F7N46_24910, F9413_19430, FVB16_00150, G4A38_21200, G4A47_21050, GQM13_22835, HIE29_ ...Gene: traT, traT_2, ACU57_00410, DTL43_23980, DU321_18605, E6D34_19660, EN85_003940, ETECE562_05006, EWK56_24090, F7N46_24910, F9413_19430, FVB16_00150, G4A38_21200, G4A47_21050, GQM13_22835, HIE29_005043, HLZ50_25370, HVW43_26420, NCTC9045_05987, OGM49_26635, RCS22_P0037, RCS51_P0105, RCS59_P0011
Production host: Escherichia coli (E. coli) / References: UniProt: Q6B3Y7
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Cryo-EM structure of the decameric TraT surface exclusion lipoprotein from Escherichia coli (F plasmid)
Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Escherichia (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 900 nm
Image recordingElectron dose: 40 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.18 / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.66 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 131705 / Symmetry type: POINT
Atomic model buildingDetails: buccaneer / Source name: Other / Type: in silico model
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00416950
ELECTRON MICROSCOPYf_angle_d0.46822900
ELECTRON MICROSCOPYf_dihedral_angle_d3.7042380
ELECTRON MICROSCOPYf_chiral_restr0.042690
ELECTRON MICROSCOPYf_plane_restr0.0022950

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