5IV8 | pdb_00005iv8

The LPS Transporter LptDE from Klebsiella pneumoniae, core complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.94 Å
  • R-Value Free: 
    0.284 (Depositor), 0.284 (DCC) 
  • R-Value Work: 
    0.235 (Depositor), 0.238 (DCC) 
  • R-Value Observed: 
    0.238 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history

Literature

Structural and Functional Characterization of the LPS Transporter LptDE from Gram-Negative Pathogens.

Botos, I.Majdalani, N.Mayclin, S.J.McCarthy, J.G.Lundquist, K.Wojtowicz, D.Barnard, T.J.Gumbart, J.C.Buchanan, S.K.

(2016) Structure 24: 965-976

  • DOI: https://doi.org/10.1016/j.str.2016.03.026
  • Primary Citation Related Structures: 
    5IV8, 5IV9, 5IVA, 5IXM

  • PubMed Abstract: 

    Incorporation of lipopolysaccharide (LPS) into the outer membrane of Gram-negative bacteria is essential for viability, and is accomplished by a two-protein complex called LptDE. We solved crystal structures of the core LptDE complexes from Yersinia pestis, Klebsiella pneumoniae, Pseudomonas aeruginosa, and a full-length structure of the K. pneumoniae LptDE complex. Our structures adopt the same plug and 26-strand β-barrel architecture found recently for the Shigella flexneri and Salmonella typhimurium LptDE structures, illustrating a conserved fold across the family. A comparison of the only two full-length structures, SfLptDE and our KpLptDE, reveals a 21° rotation of the LptD N-terminal domain that may impart flexibility on the trans-envelope LptCAD scaffold. Utilizing mutagenesis coupled to an in vivo functional assay and molecular dynamics simulations, we demonstrate the critical role of Pro231 and Pro246 in the function of the LptD lateral gate that allows partitioning of LPS into the outer membrane.


  • Organizational Affiliation
    • Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA.

Macromolecule Content 

  • Total Structure Weight: 180.4 kDa 
  • Atom Count: 11,347 
  • Modeled Residue Count: 1,390 
  • Deposited Residue Count: 1,566 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
LPS biosynthesis protein
A, C
601Klebsiella pneumoniaeMutation(s): 0 
Gene Names: AU361_02400
Membrane Entity: Yes 
UniProt
Find proteins for C4T9I0 (Klebsiella pneumoniae)
Explore C4T9I0 
Go to UniProtKB:  C4T9I0
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupC4T9I0
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
LPS-assembly lipoprotein LptE
B, D
182Klebsiella pneumoniaeMutation(s): 0 
Gene Names: lptEAPU20_03225SM74_00486SM87_01358
Membrane Entity: Yes 
UniProt
Find proteins for A0A0J4W1Y0 (Klebsiella variicola)
Explore A0A0J4W1Y0 
Go to UniProtKB:  A0A0J4W1Y0
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0J4W1Y0
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.94 Å
  • R-Value Free:  0.284 (Depositor), 0.284 (DCC) 
  • R-Value Work:  0.235 (Depositor), 0.238 (DCC) 
  • R-Value Observed: 0.238 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 75.02α = 90
b = 173.05β = 111.26
c = 84.757γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-05-18
    Type: Initial release
  • Version 1.1: 2016-05-25
    Changes: Database references
  • Version 1.2: 2016-06-15
    Changes: Database references
  • Version 1.3: 2023-09-27
    Changes: Data collection, Database references, Derived calculations, Refinement description