6MHU

Nucleotide-free Cryo-EM Structure of E.coli LptB2FG Transporter


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structural basis of lipopolysaccharide extraction by the LptB2FGC complex.

Li, Y.Orlando, B.J.Liao, M.

(2019) Nature 567: 486-490

  • DOI: https://doi.org/10.1038/s41586-019-1025-6
  • Primary Citation of Related Structures:  
    6MHU, 6MHZ, 6MI7, 6MI8

  • PubMed 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 from the inner to the outer membrane. The ATP-binding cassette transporter LptB 2 FG, which tightly associates with LptC, extracts lipopolysaccharide out of the inner membrane. The mechanism of the LptB 2 FG-LptC complex (LptB 2 FGC) and the role of LptC in lipopolysaccharide transport are poorly understood. Here we characterize the structures of LptB 2 FG and LptB 2 FGC 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 LptB 2 FGC. LptC inserts its transmembrane helix between the two transmembrane domains of LptB 2 FG, 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 LptB 2 FG in the inner membrane and Lpt protein interactions in the periplasm.


  • Organizational Affiliation

    Department of Cell Biology, Harvard Medical School, Boston, MA, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Lipopolysaccharide export system permease protein LptFA [auth F]366Escherichia coli K-12Mutation(s): 0 
Gene Names: lptFyjgPb4261JW4218
Membrane Entity: Yes 
UniProt
Find proteins for P0AF98 (Escherichia coli (strain K12))
Explore P0AF98 
Go to UniProtKB:  P0AF98
Entity Groups  
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UniProt GroupP0AF98
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Lipopolysaccharide export system permease protein LptGB [auth G]360Escherichia coli K-12Mutation(s): 0 
Gene Names: lptGyjgQb4262JW5760
Membrane Entity: Yes 
UniProt
Find proteins for P0ADC6 (Escherichia coli (strain K12))
Explore P0ADC6 
Go to UniProtKB:  P0ADC6
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UniProt GroupP0ADC6
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Lipopolysaccharide export system ATP-binding protein LptBC [auth A],
D [auth B]
251Escherichia coli K-12Mutation(s): 0 
Gene Names: lptByhbGb3201JW3168
EC: 3.6.3
Membrane Entity: Yes 
UniProt
Find proteins for P0A9V1 (Escherichia coli (strain K12))
Explore P0A9V1 
Go to UniProtKB:  P0A9V1
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UniProt GroupP0A9V1
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
JSG
Query on JSG

Download Ideal Coordinates CCD File 
E [auth G](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
C131 H240 N2 O63 P4
MVYTXVAKEAWEGM-SMTLFHDCSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01GM122797

Revision History  (Full details and data files)

  • Version 1.0: 2019-04-03
    Type: Initial release
  • Version 1.1: 2019-04-10
    Changes: Data collection, Database references
  • Version 1.2: 2019-12-18
    Changes: Author supporting evidence, Other
  • Version 1.3: 2024-03-13
    Changes: Data collection, Database references