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- PDB-9p52: LptBFGCA from Escherichia coli -

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Basic information

Entry
Database: PDB / ID: 9p52
TitleLptBFGCA from Escherichia coli
Components
  • Lipopolysaccharide export system ATP-binding protein LptB
  • Lipopolysaccharide export system permease protein LptF
  • Lipopolysaccharide export system permease protein LptG
  • Lipopolysaccharide export system protein LptC,Lipopolysaccharide export system protein LptA
KeywordsLIPID TRANSPORT / Complex / Lipopolysaccharide / ABC / ATP binding cassette / transporter
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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 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 17, 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
F: Lipopolysaccharide export system permease protein LptF
G: Lipopolysaccharide export system permease protein LptG
H: Lipopolysaccharide export system ATP-binding protein LptB


Theoretical massNumber of molelcules
Total (without water)175,2915
Polymers175,2915
Non-polymers00
Water00
1


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

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Components

#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: Expressed as a fusion with His-tagged LptA,Expressed as a fusion with His-tagged 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
#3: 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
#4: Protein Lipopolysaccharide export system permease protein LptG


Mass: 39651.410 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
Has protein modificationN

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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
1Inter-membrane lipopolysaccharide transporter composed of LptA, LptC, LptF, LptG, and two molecules of LptBCOMPLEXall0RECOMBINANT
2Inner membrane lipopolysaccharide transporter composed of LptA, LptC, LptF, LptG, and two molecules of LptBCOMPLEXall1RECOMBINANT
3Outer membrane lipopolysaccharide transporterCOMPLEX1RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
22Escherichia coli (E. coli)562
33Escherichia coli (E. coli)562
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
22Escherichia coli (E. coli)562
33Escherichia 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 8NH2C(CH2OH)31
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: 58 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: 3100000
3D reconstructionResolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 697837 / Symmetry type: POINT

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