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- PDB-6mhu: Nucleotide-free Cryo-EM Structure of E.coli LptB2FG Transporter -

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Basic information

Entry
Database: PDB / ID: 6mhu
TitleNucleotide-free Cryo-EM Structure of E.coli LptB2FG Transporter
Components
  • Lipopolysaccharide export system ATP-binding protein LptB
  • Lipopolysaccharide export system permease protein LptF
  • Lipopolysaccharide export system permease protein LptG
KeywordsTRANSPORT PROTEIN/Hydrolase / ABC transporter / lipopolysaccharide / LPS / nanodisc / TRANSPORT PROTEIN-Hydrolase complex
Function / homology
Function and homology information


Translocases; Catalysing the translocation of carbohydrates and their derivatives; Linked to the hydrolysis of a nucleoside triphosphate / transporter complex / lipopolysaccharide transport / Gram-negative-bacterium-type cell outer membrane assembly / ATP-binding cassette (ABC) transporter complex / transmembrane transport / ATP hydrolysis activity / ATP binding / membrane / plasma membrane / 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. / P-loop containing nucleotide triphosphate hydrolases / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-JSG / Lipopolysaccharide export system ATP-binding protein LptB / Lipopolysaccharide export system permease protein LptG / Lipopolysaccharide export system permease protein LptF
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4 Å
AuthorsOrlando, B.J. / Li, Y. / Liao, M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM122797 United States
CitationJournal: Nature / Year: 2019
Title: Structural basis of lipopolysaccharide extraction by the LptBFGC complex.
Authors: Yanyan Li / Benjamin J Orlando / Maofu Liao /
Abstract: In Gram-negative bacteria, lipopolysaccharide is essential for outer membrane formation and antibiotic resistance. The seven lipopolysaccharide transport (Lpt) proteins A-G move lipopolysaccharide ...In Gram-negative bacteria, lipopolysaccharide is essential for outer membrane formation and antibiotic resistance. The seven lipopolysaccharide transport (Lpt) proteins A-G move lipopolysaccharide from the inner to the outer membrane. The ATP-binding cassette transporter LptBFG, which tightly associates with LptC, extracts lipopolysaccharide out of the inner membrane. The mechanism of the LptBFG-LptC complex (LptBFGC) and the role of LptC in lipopolysaccharide transport are poorly understood. Here we characterize the structures of LptBFG and LptBFGC in nucleotide-free and vanadate-trapped states, using single-particle cryo-electron microscopy. These structures resolve the bound lipopolysaccharide, reveal transporter-lipopolysaccharide interactions with side-chain details and uncover how the capture and extrusion of lipopolysaccharide are coupled to conformational rearrangements of LptBFGC. LptC inserts its transmembrane helix between the two transmembrane domains of LptBFG, which represents a previously unknown regulatory mechanism for ATP-binding cassette transporters. Our results suggest a role for LptC in achieving efficient lipopolysaccharide transport, by coordinating the action of LptBFG in the inner membrane and Lpt protein interactions in the periplasm.
History
DepositionSep 18, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 3, 2019Provider: repository / Type: Initial release
Revision 1.0Apr 3, 2019Data content type: Additional map / Data content type: Additional map / Provider: repository / Type: Initial release
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Revision 1.0Apr 3, 2019Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Apr 3, 2019Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Apr 3, 2019Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.0Apr 3, 2019Data content type: Additional map / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Apr 3, 2019Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Apr 3, 2019Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Apr 3, 2019Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Apr 3, 2019Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.0Apr 3, 2019Data content type: Additional map / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Apr 3, 2019Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Apr 3, 2019Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Apr 3, 2019Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Apr 3, 2019Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Apr 10, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Dec 18, 2019Group: Author supporting evidence / Other / Category: atom_sites / cell / pdbx_audit_support
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] ..._atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3] / _cell.Z_PDB / _pdbx_audit_support.funding_organization
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4May 14, 2025Group: Data collection / Structure summary / Category: em_admin / em_software / pdbx_entry_details / Item: _em_admin.last_update / _em_software.name
Revision 1.1May 14, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Data processing / Experimental summary / Data content type: EM metadata / EM metadata / Category: em_admin / em_software / Data content type: EM metadata / EM metadata / Item: _em_admin.last_update / _em_software.name

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Structure visualization

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)139,2825
Polymers136,3074
Non-polymers2,9751
Water00
1


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

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Components

#1: 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 (strain K12) (bacteria)
Strain: K12 / Gene: lptF, yjgP, b4261, JW4218 / Production host: Escherichia coli (E. coli) / References: UniProt: P0AF98
#2: 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 (strain K12) (bacteria)
Strain: K12 / Gene: lptG, yjgQ, b4262, JW5760 / Production host: Escherichia coli (E. coli) / References: UniProt: P0ADC6
#3: Protein Lipopolysaccharide export system ATP-binding protein LptB


Mass: 28131.088 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: lptB, yhbG, b3201, JW3168 / Production host: Escherichia coli (E. coli)
References: UniProt: P0A9V1, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to catalyse transmembrane movement of substances
#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
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

ComponentName: LptB2FG / Type: COMPLEX / Entity ID: #1-#3 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Escherichia coli (strain K12) (bacteria) / Strain: K12
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 8
SpecimenConc.: 4 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: nanodisc incorporated LptB2FG
Specimen supportDetails: unspecified
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
MicroscopyModel: FEI POLARA 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 52 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.13_2998: / Classification: refinement
EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 103538 / Symmetry type: POINT

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