6S8N | pdb_00006s8n

Cryo-EM structure of LptB2FGC in complex with lipopolysaccharide


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 6S8N

This is version 1.2 of the entry. See complete history

Literature

Cryo-EM structures of lipopolysaccharide transporter LptB2FGC in lipopolysaccharide or AMP-PNP-bound states reveal its transport mechanism.

Tang, X.Chang, S.Luo, Q.Zhang, Z.Qiao, W.Xu, C.Zhang, C.Niu, Y.Yang, W.Wang, T.Zhang, Z.Zhu, X.Wei, X.Dong, C.Zhang, X.Dong, H.

(2019) Nat Commun 10: 4175-4175

  • DOI: https://doi.org/10.1038/s41467-019-11977-1
  • Primary Citation Related Structures: 
    6S8G, 6S8H, 6S8N

  • PubMed Abstract: 

    Lipopolysaccharides (LPS) of Gram-negative bacteria are critical for the defence against cytotoxic substances and must be transported from the inner membrane (IM) to the outer membrane (OM) through a bridge formed by seven membrane proteins (LptBFGCADE). The IM component LptB 2 FG powers the process through a yet unclarified mechanism. Here we report three high-resolution cryo-EM structures of LptB 2 FG alone and complexed with LptC (LptB 2 FGC), trapped in either the LPS- or AMP-PNP-bound state. The structures reveal conformational changes between these states and substrate binding with or without LptC. We identify two functional transmembrane arginine-containing loops interacting with the bound AMP-PNP and elucidate allosteric communications between the domains. AMP-PNP binding induces an inward rotation and shift of the transmembrane helices of LptFG and LptC to tighten the cavity, with the closure of two lateral gates, to eventually expel LPS into the bridge. Functional assays reveal the functionality of the LptF and LptG periplasmic domains. Our findings shed light on the LPS transport mechanism.


  • Organizational Affiliation
    • State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, 610041, Chengdu, China.

Macromolecule Content 

  • Total Structure Weight: 160.86 kDa 
  • Atom Count: 7,831 
  • Modeled Residue Count: 970 
  • Deposited Residue Count: 1,399 
  • Unique protein chains: 4

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Lipopolysaccharide ABC transporter, ATP-binding protein LptB
A, B
241Shigella flexneriMutation(s): 0 
Gene Names: SGF_01136
EC: 7.5.2
Membrane Entity: Yes 
UniProt
Find proteins for P0A9V4 (Shigella flexneri)
Explore P0A9V4 
Go to UniProtKB:  P0A9V4
Entity Groups
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UniProt GroupP0A9V4
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Lipopolysaccharide export system protein LptC191Shigella flexneriMutation(s): 0 
Gene Names: lptCSFxv_3552
Membrane Entity: Yes 
UniProt
Find proteins for P0ADW2 (Shigella flexneri)
Explore P0ADW2 
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UniProt GroupP0ADW2
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Lipopolysaccharide export system permease protein LptFD [auth F]366Shigella flexneriMutation(s): 0 
Gene Names: lptFSF4228S4489
Membrane Entity: Yes 
UniProt
Find proteins for P0AFA1 (Shigella flexneri)
Explore P0AFA1 
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UniProt GroupP0AFA1
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Inner membrane protein yjgQE [auth G]360Shigella flexneriMutation(s): 0 
Gene Names: yjgQS4488CQA91_25110NCTC9783_00309SAMEA3710568_03584
Membrane Entity: Yes 
UniProt
Find proteins for A0A0H2V3J7 (Shigella flexneri)
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UniProt GroupA0A0H2V3J7
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Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
L0W

Query on L0W



Download:Ideal Coordinates CCD File
I [auth G]lipopolysaccharide fragment
C95 H182 N2 O25 P2
WFPYFXOOZWPZCO-PICFCIIGSA-N
LMN

Query on LMN



Download:Ideal Coordinates CCD File
G [auth F],
J [auth G]
Lauryl Maltose Neopentyl Glycol
C47 H88 O22
MADJBYLAYPCCOO-XYPZXBMFSA-N
LMT

Query on LMT



Download:Ideal Coordinates CCD File
H [auth F],
K [auth G]
DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
DCQ

Query on DCQ



Download:Ideal Coordinates CCD File
F [auth B],
L [auth G]
2-decyl-5,6-dimethoxy-3-methylcyclohexa-2,5-diene-1,4-dione
C19 H30 O4
VMEGFMNVSYVVOM-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

Structure Validation

View Full Validation Report



Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2019-09-25
    Type: Initial release
  • Version 1.1: 2024-05-22
    Changes: Data collection, Database references
  • Version 1.2: 2025-07-02
    Changes: Data collection, Structure summary