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- EMDB-71298: LptBFGCA from Escherichia coli -

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Basic information

Entry
Database: EMDB / ID: EMD-71298
TitleLptBFGCA from Escherichia coli
Map dataUnsharpened map
Sample
  • Complex: Inter-membrane lipopolysaccharide transporter composed of LptA, LptC, LptF, LptG, and two molecules of LptB
    • Complex: Inner membrane lipopolysaccharide transporter composed of LptA, LptC, LptF, LptG, and two molecules of LptB
      • Protein or peptide: Lipopolysaccharide export system ATP-binding protein LptB
      • Protein or peptide: Lipopolysaccharide export system protein LptC,Lipopolysaccharide export system protein LptA
      • Protein or peptide: Lipopolysaccharide export system permease protein LptF
      • Protein or peptide: Lipopolysaccharide export system permease protein LptG
    • Complex: Outer membrane lipopolysaccharide transporter
KeywordsComplex / Lipopolysaccharide / ABC / ATP binding cassette / transporter / LIPID TRANSPORT
Function / homology
Function and homology information


lipopolysaccharide transfer activity / Translocases; Catalysing the translocation of carbohydrates and their derivatives; Linked to the hydrolysis of a nucleoside triphosphate / glycolipid transfer activity / transporter complex / lipopolysaccharide transport / Gram-negative-bacterium-type cell outer membrane assembly / ATP-binding cassette (ABC) transporter complex / cell outer membrane / lipopolysaccharide binding / transmembrane transport ...lipopolysaccharide transfer activity / Translocases; Catalysing the translocation of carbohydrates and their derivatives; Linked to the hydrolysis of a nucleoside triphosphate / glycolipid transfer activity / transporter complex / lipopolysaccharide transport / Gram-negative-bacterium-type cell outer membrane assembly / ATP-binding cassette (ABC) transporter complex / cell outer membrane / lipopolysaccharide binding / transmembrane transport / outer membrane-bounded periplasmic space / periplasmic space / ATP hydrolysis activity / ATP binding / membrane / identical protein binding / plasma membrane / cytoplasm
Similarity search - Function
: / Lipopolysaccharide export system protein LptA / Lipopolysaccharide assembly, LptC-related / Lipopolysaccharide export system protein LptC / : / Lipopolysaccharide-assembly, LptC-related / Permease LptG/LptF-related / LPS export ABC transporter permease LptF / LPS export ABC transporter permease LptG / Lipopolysaccharide export system permease LptF/LptG ...: / Lipopolysaccharide export system protein LptA / Lipopolysaccharide assembly, LptC-related / Lipopolysaccharide export system protein LptC / : / Lipopolysaccharide-assembly, LptC-related / 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 / : / Organic solvent tolerance-like, N-terminal / LptA/(LptD N-terminal domain) LPS transport protein / 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 ATP-binding protein LptB / Lipopolysaccharide export system permease protein LptG / Lipopolysaccharide export system protein LptA / Lipopolysaccharide export system protein LptC / Lipopolysaccharide export system permease protein LptF
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsTaylor RJ / Pahil KS / Walsh Jr RM / Kahne DE
Funding support United States, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI149778 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI081059 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI153358 United States
CitationJournal: To Be Published
Title: Structural basis for regulating lipopolysaccharide transmembrane transport
Authors: Taylor RJ / Pahil KS / Walsh Jr RM / Kahne DE
History
DepositionJun 17, 2025-
Header (metadata) releaseSep 30, 2026-
Map releaseSep 30, 2026-
UpdateSep 30, 2026-
Current statusSep 30, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_71298.png

Downloads & links

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Map

FileDownload / File: emd_71298.map.gz / Format: CCP4 / Size: 476.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationUnsharpened map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 500 pix.
= 412.5 Å		0.83 Å/pix.
x 500 pix.
= 412.5 Å		0.83 Å/pix.
x 500 pix.
= 412.5 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.825 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.35
Minimum - Maximum-0.682723 - 1.7327566
Average (Standard dev.)0.0003769458 (±0.02861219)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions500500500
Spacing500500500
CellA=B=C: 412.5 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Sharpened map

Fileemd_71298_additional_1.map
AnnotationSharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map

Fileemd_71298_half_map_1.map
AnnotationHalf map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map

Fileemd_71298_half_map_2.map
AnnotationHalf 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 : Inter-membrane lipopolysaccharide transporter composed of LptA, L...

EntireName: Inter-membrane lipopolysaccharide transporter composed of LptA, LptC, LptF, LptG, and two molecules of LptB
Components
  • Complex: Inter-membrane lipopolysaccharide transporter composed of LptA, LptC, LptF, LptG, and two molecules of LptB
    • Complex: Inner membrane lipopolysaccharide transporter composed of LptA, LptC, LptF, LptG, and two molecules of LptB
      • Protein or peptide: Lipopolysaccharide export system ATP-binding protein LptB
      • Protein or peptide: Lipopolysaccharide export system protein LptC,Lipopolysaccharide export system protein LptA
      • Protein or peptide: Lipopolysaccharide export system permease protein LptF
      • Protein or peptide: Lipopolysaccharide export system permease protein LptG
    • Complex: Outer membrane lipopolysaccharide transporter

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Supramolecule #1: Inter-membrane lipopolysaccharide transporter composed of LptA, L...

SupramoleculeName: Inter-membrane lipopolysaccharide transporter composed of LptA, LptC, LptF, LptG, and two molecules of LptB
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all

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Supramolecule #2: Inner membrane lipopolysaccharide transporter composed of LptA, L...

SupramoleculeName: Inner membrane lipopolysaccharide transporter composed of LptA, LptC, LptF, LptG, and two molecules of LptB
type: complex / ID: 2 / Parent: 1 / Macromolecule list: all
Source (natural)Organism: Escherichia coli (E. coli)

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Supramolecule #3: Outer membrane lipopolysaccharide transporter

SupramoleculeName: Outer membrane lipopolysaccharide transporter / type: complex / ID: 3 / Parent: 1
Source (natural)Organism: Escherichia coli (E. coli)

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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
EC number: Translocases; Catalysing the translocation of carbohydrates and their derivatives; Linked to the hydrolysis of a nucleoside triphosphate
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 26.593312 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: ATLTAKNLAK AYKGRRVVED VSLTVNSGEI VGLLGPNGAG KTTTFYMVVG IVPRDAGNII IDDDDISLLP LHARARRGIG YLPQEASIF RRLSVYDNLM AVLQIRDDLS AEQREDRANE LMEEFHIEHL RDSMGQSLSG GERRRVEIAR ALAANPKFIL L DEPFAGVD ...String:
ATLTAKNLAK AYKGRRVVED VSLTVNSGEI VGLLGPNGAG KTTTFYMVVG IVPRDAGNII IDDDDISLLP LHARARRGIG YLPQEASIF RRLSVYDNLM AVLQIRDDLS AEQREDRANE LMEEFHIEHL RDSMGQSLSG GERRRVEIAR ALAANPKFIL L DEPFAGVD PISVIDIKRI IEHLRDSGLG VLITDHNVRE TLAVCERAYI VSQGHLIAHG TPTEILQDEH VKRVYLGEDF R

UniProtKB: Lipopolysaccharide export system ATP-binding protein LptB

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Macromolecule #2: Lipopolysaccharide export system protein LptC,Lipopolysaccharide ...

MacromoleculeName: Lipopolysaccharide export system protein LptC,Lipopolysaccharide export system protein LptA
type: protein_or_peptide / ID: 2
Details: Expressed as a fusion with His-tagged LptA,Expressed as a fusion with His-tagged LptA
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 42.059082 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSKARRWVII VLSLAVLVMI GINMAEKDDT AQVVVNNNDP TYKSEHTDTL VYNPEGALSY RLIAQHVEYY SDQAVSWFTQ PVLTTFDKD KIPTWSVKAD KAKLTNDRML YLYGHVEVNA LVPDSQLRRI TTDNAQINLV TQDVTSEDLV TLYGTTFNSS G LKMRGNLR ...String:
MSKARRWVII VLSLAVLVMI GINMAEKDDT AQVVVNNNDP TYKSEHTDTL VYNPEGALSY RLIAQHVEYY SDQAVSWFTQ PVLTTFDKD KIPTWSVKAD KAKLTNDRML YLYGHVEVNA LVPDSQLRRI TTDNAQINLV TQDVTSEDLV TLYGTTFNSS G LKMRGNLR SKNAELIEKV RTSYEIQNKQ TQPLVPGGSG GGGSGGGGSG GGGSVTGDTD QPIHIESDQQ SLDMQGNVVT FT GNVIVTQ GTIKINADKV VVTRPGGEQG KEVIDGYGKP ATFYQMQDNG KPVEGHASQM HYELAKDFVV LTGNAYLQQV DSN IKGDKI TYLVKEQKMQ AFSDKGKRVT TVLVPSQLQD KNNKGQTPAQ KKGNLVPRGS HHHHHHH

UniProtKB: Lipopolysaccharide export system protein LptC, Lipopolysaccharide export system protein LptA

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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: Escherichia coli (E. coli)
Molecular weightTheoretical: 40.393473 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MIIIRYLVRE TLKSQLAILF ILLLIFFCQK LVRILGAAVD GDIPANLVLS LLGLGVPEMA QLILPLSLFL GLLMTLGKLY TESEITVMH ACGLSKAVLV KAAMILAVFT AIVAAVNVMW AGPWSSRHQD EVLAEAKANP GMAALAQGQF QQATNGSSVL F IESVDGSD ...String:
MIIIRYLVRE TLKSQLAILF ILLLIFFCQK LVRILGAAVD GDIPANLVLS LLGLGVPEMA QLILPLSLFL GLLMTLGKLY TESEITVMH ACGLSKAVLV KAAMILAVFT AIVAAVNVMW AGPWSSRHQD EVLAEAKANP GMAALAQGQF QQATNGSSVL F IESVDGSD FKDVFLAQIR PKGNARPSVV VADSGHLTQL RDGSQVVTLN QGTRFEGTAL LRDFRITDFQ DYQAIIGHQA VA LDPNDTD QMDMRTLWNT DTDRARAELN WRITLVFTVF MMALMVVPLS VVNPRQGRVL SMLPAMLLYL LFFLIQTSLK SNG GKGKLD PTLWMWTVNL IYLALAIVLN LWDTVPVRRL RASFSRKGAV

UniProtKB: Lipopolysaccharide export system permease protein LptF

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Macromolecule #4: Lipopolysaccharide export system permease protein LptG

MacromoleculeName: Lipopolysaccharide export system permease protein LptG
type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 39.65141 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MQPFGVLDRY IGKTIFTTIM MTLFMLVSLS GIIKFVDQLK KAGQGSYDAL GAGMYTLLSV PKDVQIFFPM AALLGALLGL GMLAQRSEL VVMQASGFTR MQVALSVMKT AIPLVLLTMA IGEWVAPQGE QMARNYRAQA MYGGSLLSTQ QGLWAKDGNN F VYIERVKG ...String:
MQPFGVLDRY IGKTIFTTIM MTLFMLVSLS GIIKFVDQLK KAGQGSYDAL GAGMYTLLSV PKDVQIFFPM AALLGALLGL GMLAQRSEL VVMQASGFTR MQVALSVMKT AIPLVLLTMA IGEWVAPQGE QMARNYRAQA MYGGSLLSTQ QGLWAKDGNN F VYIERVKG DEELGGISIY AFNENRRLQS VRYAATAKFD PEHKVWRLSQ VDESDLTNPK QITGSQTVSG TWKTNLTPDK LG VVALDPD ALSISGLHNY VKYLKSSGQD AGRYQLNMWS KIFQPLSVAV MMLMALSFIF GPLRSVPMGV RVVTGISFGF VFY VLDQIF GPLTLVYGIP PIIGALLPSA SFFLISLWLL MRKS

UniProtKB: Lipopolysaccharide export system permease protein LptG

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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: 8
Component:
ConcentrationFormulaName
20.0 mMNH2C(CH2OH)3Tris pH 8
150.0 mMNaClSodium Chloride
0.02 %C56H92O25glyco-diosgenin
1.0 %C3H8O3glycerol
1.0 %C2H6OSDMSO
1.0 %C2H6O2ethylene glycol

Details: 20mM Tris HCl, 150mM NaCl, 1% glycerol, 1% DMSO, 1% ethylene glycol, 0.02% GDN
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV
DetailsThis sample was monodisperse as determined by SEC.

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOCONTINUUM (6k x 4k) / Average electron dose: 58.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.1 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 3100000
CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Details: Ab initio model generated based on the data using cryoSPARC
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 697837
Initial angle assignmentType: RANDOM ASSIGNMENT / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final 3D classificationSoftware - Name: cryoSPARC
FSC plot (resolution estimation)

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