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- EMDB-47084: Cryo-EM structure of LptB2FG apo-1 -

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Basic information

Entry
Database: EMDB / ID: EMD-47084
TitleCryo-EM structure of LptB2FG apo-1
Map data
Sample
  • Complex: LptB2FG
    • Protein or peptide: Lipopolysaccharide export system ATP-binding protein LptB
    • Protein or peptide: Permease
    • Protein or peptide: Lipopolysaccharide export system permease protein LptF
  • Ligand: 1,2-Distearoyl-sn-glycerophosphoethanolamine
KeywordsLPS transporter / LIPID TRANSPORT
Function / homology
Function and homology information


lipopolysaccharide transport / ATP-binding cassette (ABC) transporter complex / transmembrane transport / ATP hydrolysis activity / ATP binding / cytoplasm
Similarity search - Function
Permease LptG/LptF-related / LPS export ABC transporter permease LptF / LPS export ABC transporter permease LptG / Lipopolysaccharide export system permease LptF/LptG / Branched-chain amino acid ATP-binding cassette transporter, C-terminal / Branched-chain amino acid ATP-binding cassette transporter / LPS export ABC transporter, ATP-binding protein LptB / : / ABC transporter-like, conserved site / ABC transporters family signature. ...Permease LptG/LptF-related / LPS export ABC transporter permease LptF / LPS export ABC transporter permease LptG / Lipopolysaccharide export system permease LptF/LptG / Branched-chain amino acid ATP-binding cassette transporter, C-terminal / Branched-chain amino acid ATP-binding cassette transporter / LPS export ABC transporter, ATP-binding protein LptB / : / ABC transporter-like, conserved site / ABC transporters family signature. / ABC transporter / ABC transporter-like, ATP-binding domain / ATP-binding cassette, ABC transporter-type domain profile. / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Lipopolysaccharide export system permease protein LptF / Lipopolysaccharide export system ATP-binding protein LptB / LPS export ABC transporter permease LptG
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.34 Å
AuthorsSu C
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: Nat Commun / Year: 2025
Title: Structural snapshots of Pseudomonas aeruginosa LptBFG and LptBFGC reveal insights into lipopolysaccharide recognition and transport.
Authors: Francesco Fiorentino / Matteo Cervoni / Yi Wang / Leonhard H Urner / Joshua B Sauer / Anh Tran / Robin A Corey / Dante Rotili / Antonello Mai / Phillip J Stansfeld / Francesco Imperi / ...Authors: Francesco Fiorentino / Matteo Cervoni / Yi Wang / Leonhard H Urner / Joshua B Sauer / Anh Tran / Robin A Corey / Dante Rotili / Antonello Mai / Phillip J Stansfeld / Francesco Imperi / Edward W Yu / Chih-Chia Su / Carol V Robinson / Jani R Bolla /
Abstract: Gram-negative bacteria are intrinsically resistant to many antibiotics because of densely packed lipopolysaccharides (LPS) in the outer leaflet of their outer membrane (OM), which acts as a highly ...Gram-negative bacteria are intrinsically resistant to many antibiotics because of densely packed lipopolysaccharides (LPS) in the outer leaflet of their outer membrane (OM), which acts as a highly effective barrier towards the spontaneous permeation of toxic molecules, including antibiotics. LPS are extracted from the inner membrane by the ABC transporter LptBFGC and translocated across the periplasm via a protein bridge to the OM. While structural studies have elucidated aspects of Lpt function in enterobacteria, little is known about how this system operates in divergent species such as Pseudomonas aeruginosa, a major human pathogen. Here, we report five cryo-electron microscopy structures of P. aeruginosa LptBFG and LptBFGC, revealing a rigid body movement in the periplasmic β-jellyroll domains necessary for LPS to shuttle through the periplasmic space. Notably, these structures exhibit a significantly smaller LPS binding cavity compared to previously determined models, suggesting the ligand-unbound states of the transporter. Mass spectrometry and molecular dynamics simulations indicate that the phosphate groups of LPS are the key determinants for binding and that the transporter can also accommodate cardiolipin. Together, these findings reveal previously unappreciated structural diversity in the Lpt system and provide mechanistic insight into how pathogenic Gram-negative bacteria tailor LPS recognition and transport. This understanding offers new avenues for the development of novel inhibitors targeting membrane biogenesis.
History
DepositionSep 19, 2024-
Header (metadata) releaseNov 19, 2025-
Map releaseNov 19, 2025-
UpdateDec 31, 2025-
Current statusDec 31, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_47084.png

Downloads & links

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Map

FileDownload / File: emd_47084.map.gz / Format: CCP4 / Size: 163.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 350 pix.
= 378. Å		1.08 Å/pix.
x 350 pix.
= 378. Å		1.08 Å/pix.
x 350 pix.
= 378. Å

Surface

Projections

Slices (1/3)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.08 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-0.55200213 - 1.4584416
Average (Standard dev.)0.00082290085 (±0.02790592)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions350350350
Spacing350350350
CellA=B=C: 378.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_47084_additional_1.map
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Half map: #2

Fileemd_47084_half_map_1.map
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Half map: #1

Fileemd_47084_half_map_2.map
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Sample components

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Entire : LptB2FG

EntireName: LptB2FG
Components
  • Complex: LptB2FG
    • Protein or peptide: Lipopolysaccharide export system ATP-binding protein LptB
    • Protein or peptide: Permease
    • Protein or peptide: Lipopolysaccharide export system permease protein LptF
  • Ligand: 1,2-Distearoyl-sn-glycerophosphoethanolamine

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Supramolecule #1: LptB2FG

SupramoleculeName: LptB2FG / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Pseudomonas aeruginosa (bacteria)

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Macromolecule #1: Lipopolysaccharide export system ATP-binding protein LptB

MacromoleculeName: Lipopolysaccharide export system ATP-binding protein LptB
type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas aeruginosa (bacteria)
Molecular weightTheoretical: 27.833975 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGSMATLKAQ HLAKSYKGRQ VVRDVSMSID SGQIVGLLGP NGAGKTTCFY MIVGLVQADQ GVVRIDEQNV THLPMHGRAR AGIGYLPQE ASIFRKLSVS DNIMAILETR SDLDRNGRKE ALEGLLQEFH IHHIRDNLGM SLSGGERRRV EIARALASAP K FILLDEPF ...String:
MGSMATLKAQ HLAKSYKGRQ VVRDVSMSID SGQIVGLLGP NGAGKTTCFY MIVGLVQADQ GVVRIDEQNV THLPMHGRAR AGIGYLPQE ASIFRKLSVS DNIMAILETR SDLDRNGRKE ALEGLLQEFH IHHIRDNLGM SLSGGERRRV EIARALASAP K FILLDEPF AGVDPISVGD IKQIIHHLKA KGIGILITDH NVRETLDICE TAYIVNDGQL IAEGDAESIL ANDLVKEVYL GH EFRLKLH HHHHH

UniProtKB: Lipopolysaccharide export system ATP-binding protein LptB

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Macromolecule #2: Permease

MacromoleculeName: Permease / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas aeruginosa (bacteria)
Molecular weightTheoretical: 39.511086 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGSMVKLDRY IGVTVFVAIL AVLGVILGLA LLFAFIDELN DISASYGIGD ALRFIFLTAP RRAYDMLPMA ALIGCLVGLG TLASNSELT IMRAAGVSLS RIVWAVMKPM LVLMLAGILV GEYVAPWTEN IAQSGRALAQ GGGDSQSSKR GLWHRQGREY I HINAVQPN ...String:
MGSMVKLDRY IGVTVFVAIL AVLGVILGLA LLFAFIDELN DISASYGIGD ALRFIFLTAP RRAYDMLPMA ALIGCLVGLG TLASNSELT IMRAAGVSLS RIVWAVMKPM LVLMLAGILV GEYVAPWTEN IAQSGRALAQ GGGDSQSSKR GLWHRQGREY I HINAVQPN GVLYGVTRYR FDEQRGLESA SFAKRARFET DHWQLEEVTT TLLHPREKRS EVVKLPTERW DAQLSPQLLN TV VMEPEAL SISGLWQYIH YLADQGLNNN RYWLAFWTKV LQPLVTAALV LMAISFIFGP LRSVTLGQRI FTGVLVGFVF RIA QDLLGP SSLVFDFPPL LAVVIPASIC ALAGVWLLRR AG

UniProtKB: LPS export ABC transporter permease LptG

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Macromolecule #3: Lipopolysaccharide export system permease protein LptF

MacromoleculeName: Lipopolysaccharide export system permease protein LptF
type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas aeruginosa (bacteria)
Molecular weightTheoretical: 41.643719 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGSMIVFRYL SREVLVTMSA VSAVLLVIIM SGRFIKYLAQ AAQGLLDPGS LFLIMAFRIP GFLQLILPLG LFLGILLAYG RLYLESEMT VLSATGMSQK RLLGYTMAPA LLVAILVAWL SLFLAPQGIN QFALLLNKQD TLTEFDTLVP GRFQAMRDGT R VTYTEELS ...String:
MGSMIVFRYL SREVLVTMSA VSAVLLVIIM SGRFIKYLAQ AAQGLLDPGS LFLIMAFRIP GFLQLILPLG LFLGILLAYG RLYLESEMT VLSATGMSQK RLLGYTMAPA LLVAILVAWL SLFLAPQGIN QFALLLNKQD TLTEFDTLVP GRFQAMRDGT R VTYTEELS KDRGELAGIF ISQKDLNSSN QERGISILVA EKGTQNIQAD GSRYLILHNG YRYDGNPGQA NYRAIQYDTY GV MLPKPEA SSEVSERDAV PTADLFGSDN PRYQAELQWR LSTPLLVFVV TLLAVPLSRV NPRQGRFLKL LPAILLYMGY LAL LIAVRG QLDKGKIPMA IGLWWVHGLF LAIGLLLFYW EPLRLKLASS RAGREVAHG

UniProtKB: Lipopolysaccharide export system permease protein LptF

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Macromolecule #4: 1,2-Distearoyl-sn-glycerophosphoethanolamine

MacromoleculeName: 1,2-Distearoyl-sn-glycerophosphoethanolamine / type: ligand / ID: 4 / Number of copies: 3 / Formula: 3PE
Molecular weightTheoretical: 748.065 Da
Chemical component information

ChemComp-3PE:
1,2-Distearoyl-sn-glycerophosphoethanolamine / phospholipid*YM

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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

Concentration0.5 mg/mL
BufferpH: 7.5
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV
DetailsThis is from a heterogeneous and impure protein sample.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 29.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 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: INSILICO MODEL / In silico model: ab initio reconstruction by cryosparc
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.34 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 66740
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementProtocol: AB INITIO MODEL
Output model

PDB-9doh:
Cryo-EM structure of LptB2FG apo-1

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