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- PDB-9p7p: LPS transport bridge LptBFGCADE from Escherichia coli in complex ... -

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Basic information

Entry
Database: PDB / ID: 9p7p
TitleLPS transport bridge LptBFGCADE from Escherichia coli in complex with lipopolysaccharide
Components
  • (LPS-assembly ...) x 2
  • (Lipopolysaccharide export system ...) x 4
KeywordsLIPID TRANSPORT / Complex / Lipopolysaccharide / ABC / ATP binding cassette / transporter / bridge / intermembrane
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 / LptD, C-terminal / LPS-assembly protein LptD / : / LPS transport system D / 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 / : / LPS-assembly lipoprotein LptE / Lipopolysaccharide-assembly / 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. / Prokaryotic membrane lipoprotein lipid attachment site profile. / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Chem-JSG / Lipopolysaccharide export system ATP-binding protein LptB / LPS-assembly lipoprotein LptE / Lipopolysaccharide export system permease protein LptG / Lipopolysaccharide export system protein LptA / Lipopolysaccharide export system protein LptC / Lipopolysaccharide export system permease protein LptF / LPS-assembly protein LptD
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsTaylor, R.J. / Pahil, K.S. / Walsh Jr., R.M. / Kahne, D.E.
Funding support United States, 3items
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, R.J. / Pahil, K.S. / Walsh Jr., R.M. / Kahne, D.E.
History
DepositionJun 20, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 30, 2026Provider: repository / Type: Initial release
Revision 1.0Sep 30, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Lipopolysaccharide export system ATP-binding protein LptB
C: Lipopolysaccharide export system protein LptC,Lipopolysaccharide export system protein LptA
D: LPS-assembly protein LptD
E: LPS-assembly lipoprotein LptE
F: Lipopolysaccharide export system permease protein LptF
G: Lipopolysaccharide export system permease protein LptG
H: Lipopolysaccharide export system ATP-binding protein LptB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)282,0878
Polymers279,1127
Non-polymers2,9751
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Lipopolysaccharide export system ... , 4 types, 5 molecules BHCFG

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


Mass: 26593.312 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: lptB, yhbG, b3201, JW3168 / Production host: Escherichia coli (E. coli)
References: UniProt: P0A9V1, Translocases; Catalysing the translocation of carbohydrates and their derivatives; Linked to the hydrolysis of a nucleoside triphosphate
#2: Protein Lipopolysaccharide export system protein LptC,Lipopolysaccharide export system protein LptA


Mass: 42059.082 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: LptC expressed as a fusion protein with LptA / Source: (gene. exp.) Escherichia coli (E. coli) / Gene: lptC, yrbK, b3199, JW3166, lptA, yhbN, b3200, JW3167 / Production host: Escherichia coli (E. coli) / References: UniProt: P0ADV9, UniProt: P0ADV1
#5: Protein Lipopolysaccharide export system permease protein LptF


Mass: 40393.473 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: lptF, yjgP, b4261, JW4218 / Production host: Escherichia coli (E. coli) / References: UniProt: P0AF98
#6: Protein Lipopolysaccharide export system permease protein LptG


Mass: 39392.090 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: lptG, yjgQ, b4262, JW5760 / Production host: Escherichia coli (E. coli) / References: UniProt: P0ADC6

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LPS-assembly ... , 2 types, 2 molecules DE

#3: Protein LPS-assembly protein LptD / Organic solvent tolerance protein


Mass: 87078.438 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: lptD, imp, ostA, yabG, b0054, JW0053 / Production host: Escherichia coli (E. coli) / References: UniProt: P31554
#4: Protein LPS-assembly lipoprotein LptE / Rare lipoprotein B


Mass: 17002.602 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: lptE, rlpB, b0641, JW0636 / Production host: Escherichia coli (E. coli) / References: UniProt: P0ADC1

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Non-polymers , 1 types, 1 molecules

#7: Chemical ChemComp-JSG / (2~{R},4~{R},5~{R},6~{R})-6-[(1~{R})-1,2-bis(oxidanyl)ethyl]-2-[(2~{R},4~{R},5~{R},6~{R})-6-[(1~{R})-1,2-bis(oxidanyl)ethyl]-5-[(2~{S},3~{S},4~{R},5~{R},6~{R})-6-[(1~{S})-1,2-bis(oxidanyl)ethyl]-4-[(2~{R},3~{S},4~{R},5~{S},6~{R})-6-[(1~{S})-2-[(2~{S},3~{S},4~{S},5~{S},6~{R})-6-[(1~{S})-1,2-bis(oxidanyl)ethyl]-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-1-oxidanyl-ethyl]-3,4-bis(oxidanyl)-5-phosphonooxy-oxan-2-yl]oxy-3-oxidanyl-5-phosphonooxy-oxan-2-yl]oxy-2-carboxy-2-[[(2~{R},3~{S},4~{R},5~{R},6~{R})-5-[[(3~{R})-3-dodecanoyloxytetradecanoyl]amino]-6-[[(2~{R},3~{S},4~{R},5~{R},6~{R})-3-oxidanyl-5-[[(3~{R})-3-oxidanyltetradecanoyl]amino]-4-[(3~{R})-3-oxidanyltetradecanoyl]oxy-6-phosphonooxy-oxan-2-yl]methoxy]-3-phosphonooxy-4-[(3~{R})-3-tetradecanoyloxytetradecanoyl]oxy-oxan-2-yl]methoxy]oxan-4-yl]oxy-4,5-bis(oxidanyl)oxane-2-carboxylic acid


Mass: 2975.178 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C131H240N2O63P4 / Feature type: SUBJECT OF INVESTIGATION

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Details

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

Component
IDNameTypeEntity IDParent-IDSource
1Intermembrane lipopolysaccharide transport bridge composed of LptD, LptE, LptC-LptA fusion protein, LptF, LptG, and two molecules of LptB in complex with lipopolysaccharideCOMPLEX#2, #1, #3-#60RECOMBINANT
2Inner membrane portion of lipopolysaccharide transporterCOMPLEX#2, #1, #5-#61RECOMBINANT
3Outer membrane portion of lipopolysaccharide transporter with LptACOMPLEX#2-#41RECOMBINANT
Molecular weight
IDEntity assembly-IDExperimental value
11NO
21NO
33
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
32Escherichia coli (E. coli)562
43Escherichia coli (E. coli)562
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
32Escherichia coli (E. coli)562
43Escherichia coli (E. coli)562
Buffer solutionpH: 8
Details: 20mM Tris HCl, 150mM NaCl, 1% glycerol, 1% DMSO, 1% ethylene glycol, 0.02% GDN
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMTris pH 8C(CH2OH)3NH21
2150 mMSodium ChlorideNaCl1
30.02 %glyco-diosgeninC56H92O251
41 %glycerolC3H8O31
51 %DMSOC2H6OS1
61 %ethylene glycolC2H6O21
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: This sample was monodisperse as determined by SEC.
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2200 nm / Nominal defocus min: 1100 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOCONTINUUM (6k x 4k)

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
2SerialEMimage acquisition
4cryoSPARCCTF correction
10cryoSPARCinitial Euler assignment
11cryoSPARCfinal Euler assignment
12cryoSPARCclassification
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 666000
3D reconstructionResolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 157094
Details: This is a composite map; the component maps are ~3.3-3.4A resolution.
Symmetry type: POINT

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