6MI8 | pdb_00006mi8

Cryo-EM Structure of vanadate-trapped E.coli LptB2FGC


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

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This is version 1.4 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 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.

Macromolecule Content 

  • Total Structure Weight: 137.4 kDa 
  • Atom Count: 7,139 
  • Modeled Residue Count: 911 
  • Deposited Residue Count: 1,228 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Lipopolysaccharide export system ATP-binding protein LptB
A, B
251Escherichia coli K-12Mutation(s): 0 
Gene Names: lptByhbGb3201JW3168
EC: 3.6.3 (PDB Primary Data), 7.5.2 (UniProt)
Membrane Entity: Yes 
UniProt
Find proteins for P0A9V1 (Escherichia coli (strain K12))
Explore P0A9V1 
Go to UniProtKB:  P0A9V1
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A9V1
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Lipopolysaccharide export system permease protein LptFC [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
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Lipopolysaccharide export system permease protein LptGD [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
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0ADC6
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

Structure Validation

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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
  • Version 1.4: 2025-06-04
    Changes: Data collection, Structure summary