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- EMDB-47085: Cryo-EM structure of LptB2FG apo-II -

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Basic information

Entry
Database: EMDB / ID: EMD-47085
TitleCryo-EM structure of LptB2FG apo-II
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: 3.26 Å
AuthorsSu CC
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: To Be Published
Title: Structural snapshots of Pseudomonas aeruginosa LptB2FG and LptB2FGC reveal insights into lipopolysaccharide recognition and transport
Authors: Su C
History
DepositionSep 19, 2024-
Header (metadata) releaseNov 19, 2025-
Map releaseNov 19, 2025-
UpdateNov 19, 2025-
Current statusNov 19, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_47085.png

Downloads & links

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Map

FileDownload / File: emd_47085.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

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Slices (1/3)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.08 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-1.7222254 - 2.524776
Average (Standard dev.)0.00071089756 (±0.038933802)
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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Mask #1

Fileemd_47085_msk_1.map
Projections & Slices
AxesZYX

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Additional map: #1

Fileemd_47085_additional_1.map
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Half map: #1

Fileemd_47085_half_map_1.map
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Half map: #2

Fileemd_47085_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: 4 / 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: 3.26 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 298102
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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Atomic model buiding 1

RefinementProtocol: AB INITIO MODEL
Output model

PDB-9dok:
Cryo-EM structure of LptB2FG apo-II

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