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

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Basic information

Entry
Database: PDB / ID: 9fsm
TitleCryo-EM structure of the decameric TraT surface exclusion lipoprotein from Klebsiella pneumoniae (pKpQIL 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 / DIACYL GLYCEROL / TraT complement resistance protein
Function and homology information
Biological speciesKlebsiella pneumoniae (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.47 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 21, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)246,15020
Polymers239,90010
Non-polymers6,25010
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, initial map showed 10-fold symmetry, gel filtration, elution as a decamer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
TraT complement resistance protein


Mass: 23989.965 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Details: (DGA) corresponds to the posttranslational modification by diacylglycerol (DAG) The last 3 residues GSG are from the expression tag.
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: G9G2A5
#2: Chemical
ChemComp-DGA / DIACYL GLYCEROL


Mass: 625.018 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C39H76O5 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationY

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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 Klebsiella pneumoniae (pKpQIL plasmid)
Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Klebsiella pneumoniae (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: TFS FALCON 4i (4k 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: 2.47 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 210600 / Symmetry type: POINT
Atomic model buildingDetails: buccaneer / Source name: Other / Type: in silico model
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00617240
ELECTRON MICROSCOPYf_angle_d0.5923290
ELECTRON MICROSCOPYf_dihedral_angle_d12.7932600
ELECTRON MICROSCOPYf_chiral_restr0.0432740
ELECTRON MICROSCOPYf_plane_restr0.0033000

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