7EFO

LptB2FG-LPS from Klebsiella pneumoniae in nanodiscs


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.85 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


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Literature

Cryo-EM structures of LptB 2 FG and LptB 2 FGC from Klebsiella pneumoniae in complex with lipopolysaccharide.

Luo, Q.Shi, H.Xu, X.

(2021) Biochem Biophys Res Commun 571: 20-25

  • DOI: https://doi.org/10.1016/j.bbrc.2021.07.049
  • Primary Citation of Related Structures:  
    7EFO

  • PubMed 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 transport proteins (LptA-G). LptB 2 FG, 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 LptB 2 FG and LptB 2 FGC from Klebsiella pneumoniae in complex with LPS. The KpLptB 2 FG-LPS structure provides detailed interactions between LPS and the transporter, while the KpLptB 2 FGC-LPS structure may represent an intermediate state that the transmembrane helix of LptC has not been fully inserted into the transmembrane domains of LptB 2 FG.


  • Organizational Affiliation

    Department of Clinical Laboratory, Shenzhen Baoan Women's and Children's Hospital, Jinan University, Shenzhen, 518133, China; National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China. Electronic address: luoqingshan@moon.ibp.ac.cn.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Lipopolysaccharide export system ATP-binding protein LptB
A, B
241Klebsiella pneumoniae subsp. pneumoniaeMutation(s): 0 
Gene Names: lptB_3lptB
Membrane Entity: Yes 
UniProt
Find proteins for A0A2X3II39 (Klebsiella pneumoniae subsp. pneumoniae)
Explore A0A2X3II39 
Go to UniProtKB:  A0A2X3II39
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A2X3II39
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Lipopolysaccharide export system permease protein LptFC [auth F]365Klebsiella pneumoniae subsp. pneumoniaeMutation(s): 0 
Gene Names: lptF
Membrane Entity: Yes 
UniProt
Find proteins for A0A1Y0Q3P9 (Klebsiella pneumoniae subsp. pneumoniae)
Explore A0A1Y0Q3P9 
Go to UniProtKB:  A0A1Y0Q3P9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1Y0Q3P9
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
LPS export ABC transporter permease LptGD [auth G]360Klebsiella pneumoniae subsp. pneumoniaeMutation(s): 0 
Gene Names: lptG
Membrane Entity: Yes 
UniProt
Find proteins for A0A1Y0Q3C0 (Klebsiella pneumoniae subsp. pneumoniae)
Explore A0A1Y0Q3C0 
Go to UniProtKB:  A0A1Y0Q3C0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1Y0Q3C0
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
JSG (Subject of Investigation/LOI)
Query on JSG

Download Ideal Coordinates CCD File 
E [auth F](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: 3.85 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Science and Technology (MoST, China)China2016YFA0500404
Chinese Academy of SciencesChinaXDB37020201
National Natural Science Foundation of China (NSFC)China31625009

Revision History  (Full details and data files)

  • Version 1.0: 2022-03-02
    Type: Initial release