4M4D

Crystal structure of lipopolysaccharide binding protein


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.909 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.230 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

The crystal structure of lipopolysaccharide binding protein reveals the location of a frequent mutation that impairs innate immunity.

Eckert, J.K.Kim, Y.J.Kim, J.I.Gurtler, K.Oh, D.Y.Sur, S.Lundvall, L.Hamann, L.van der Ploeg, A.Pickkers, P.Giamarellos-Bourboulis, E.Kubarenko, A.V.Weber, A.N.Kabesch, M.Kumpf, O.An, H.J.Lee, J.O.Schumann, R.R.

(2013) Immunity 39: 647-660

  • DOI: 10.1016/j.immuni.2013.09.005

  • PubMed Abstract: 
  • Lipopolysaccharide (LPS) binding protein (LBP) is an acute-phase protein that initiates an immune response after recognition of bacterial LPS. Here, we report the crystal structure of murine LBP at 2.9 Å resolution. Several structural differences wer ...

    Lipopolysaccharide (LPS) binding protein (LBP) is an acute-phase protein that initiates an immune response after recognition of bacterial LPS. Here, we report the crystal structure of murine LBP at 2.9 Å resolution. Several structural differences were observed between LBP and the related bactericidal/permeability-increasing protein (BPI), and the LBP C-terminal domain contained a negatively charged groove and a hydrophobic "phenylalanine core." A frequent human LBP SNP (allelic frequency 0.08) affected this region, potentially generating a proteinase cleavage site. The mutant protein had a reduced binding capacity for LPS and lipopeptides. SNP carriers displayed a reduced cytokine response after in vivo LPS exposure and lower cytokine concentrations in pneumonia. In a retrospective trial, the LBP SNP was associated with increased mortality rates during sepsis and pneumonia. Thus, the structural integrity of LBP may be crucial for fighting infections efficiently, and future patient stratification might help to develop better therapeutic strategies.


    Organizational Affiliation

    Institute for Microbiology and Hygiene, Charité-Universitätsmedizin Berlin, 10117 Berlin, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Lipopolysaccharide-binding protein
A, B
467Mus musculusMutation(s): 0 
Gene Names: Lbp
Find proteins for Q61805 (Mus musculus)
Go to UniProtKB:  Q61805
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PC1
Query on PC1

Download SDF File 
Download CCD File 
A, B
1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE
3-SN-PHOSPHATIDYLCHOLINE
C44 H88 N O8 P
NRJAVPSFFCBXDT-HUESYALOSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
A, B
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.909 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.230 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 77.282α = 90.00
b = 59.906β = 102.63
c = 119.932γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data collection
PHASERphasing
PHENIXrefinement
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Revision History 

  • Version 1.0: 2013-10-30
    Type: Initial release
  • Version 1.1: 2015-06-17
    Type: Database references