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- PDB-7efo: LptB2FG-LPS from Klebsiella pneumoniae in nanodiscs -

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Basic information

Entry
Database: PDB / ID: 7efo
TitleLptB2FG-LPS from Klebsiella pneumoniae in nanodiscs
Components
  • LPS export ABC transporter permease LptG
  • Lipopolysaccharide export system ATP-binding protein LptB
  • Lipopolysaccharide export system permease protein LptF
KeywordsMEMBRANE PROTEIN / ABC transporter
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
Chem-JSG / Permease / Lipopolysaccharide export system permease protein LptF / Lipopolysaccharide export system ATP-binding protein LptB
Similarity search - Component
Biological speciesKlebsiella pneumoniae subsp. pneumoniae (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.85 Å
AuthorsLuo, Q. / Shi, H.
Funding support China, 3items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2016YFA0500404 China
Chinese Academy of SciencesXDB37020201 China
National Natural Science Foundation of China (NSFC)31625009 China
CitationJournal: Biochem Biophys Res Commun / Year: 2021
Title: Cryo-EM structures of LptBFG and LptBFGC from Klebsiella pneumoniae in complex with lipopolysaccharide.
Authors: Qingshan Luo / Huigang Shi / Xueqing Xu /
Abstract: Lipopolysaccharide (LPS) is an essential component of the outer membrane (OM) in most Gram-negative bacteria. LPS transport from the inner membrane (IM) to the OM is achieved by seven ...Lipopolysaccharide (LPS) is an essential component of the outer membrane (OM) in most Gram-negative bacteria. LPS transport from the inner membrane (IM) to the OM is achieved by seven lipopolysaccharide transport proteins (LptA-G). LptBFG, an type VI ATP-binding cassette (ABC) transporter, forms a stable complex with LptC, extracts LPS from the IM and powers LPS transport to the OM. Here we report the cryo-EM structures of LptBFG and LptBFGC from Klebsiella pneumoniae in complex with LPS. The KpLptBFG-LPS structure provides detailed interactions between LPS and the transporter, while the KpLptBFGC-LPS structure may represent an intermediate state that the transmembrane helix of LptC has not been fully inserted into the transmembrane domains of LptBFG.
History
DepositionMar 22, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 2, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 5, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Assembly

Deposited unit
A: Lipopolysaccharide export system ATP-binding protein LptB
B: Lipopolysaccharide export system ATP-binding protein LptB
F: Lipopolysaccharide export system permease protein LptF
G: LPS export ABC transporter permease LptG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,8295
Polymers133,8544
Non-polymers2,9751
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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


Mass: 26879.768 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae subsp. pneumoniae (bacteria)
Gene: lptB_3, lptB / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2X3II39
#2: Protein Lipopolysaccharide export system permease protein LptF


Mass: 40431.551 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae subsp. pneumoniae (bacteria)
Gene: lptF / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1Y0Q3P9
#3: Protein LPS export ABC transporter permease LptG / Lipopolysaccharide ABC transporter permease LptG / Permease


Mass: 39662.438 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae subsp. pneumoniae (bacteria)
Gene: lptG / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1Y0Q3C0
#4: 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: obtained synthetically / Formula: C131H240N2O63P4 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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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

ComponentName: LptB2FG from Klebsiella pneumoniae with bound LPS / Type: COMPLEX / Entity ID: #1-#3 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Klebsiella pneumoniae subsp. pneumoniae 1158 (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid type: Quantifoil R2/2
VitrificationInstrument: LEICA EM GP / Cryogen name: NITROGEN / Humidity: 100 % / Chamber temperature: 283 K

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Electron microscopy imaging

MicroscopyModel: FEI TITAN
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: 1400 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K2 BASE (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.19.1_4122: / Classification: refinement
CTF correctionType: NONE
3D reconstructionResolution: 3.85 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 71000 / Symmetry type: POINT

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