4M4D | pdb_00004m4d

Crystal structure of lipopolysaccharide binding protein


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.91 Å
  • R-Value Free: 
    0.277 (Depositor), 0.276 (DCC) 
  • R-Value Work: 
    0.230 (Depositor), 0.225 (DCC) 
  • R-Value Observed: 
    0.232 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.4 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: https://doi.org/10.1016/j.immuni.2013.09.005
  • Primary Citation Related Structures: 
    4M4D

  • 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 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.

Macromolecule Content 

  • Total Structure Weight: 107.41 kDa 
  • Atom Count: 7,212 
  • Modeled Residue Count: 890 
  • Deposited Residue Count: 934 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Lipopolysaccharide-binding protein
A, B
467Mus musculusMutation(s): 0 
Gene Names: Lbp
UniProt & NIH Common Fund Data Resources
Find proteins for Q61805 (Mus musculus)
Explore Q61805 
Go to UniProtKB:  Q61805
IMPC:  MGI:1098776
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ61805
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PC1

Query on PC1



Download:Ideal Coordinates CCD File
H [auth A],
I [auth B]
1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE
C44 H88 N O8 P
NRJAVPSFFCBXDT-HUESYALOSA-N
NAG

Query on NAG



Download:Ideal Coordinates CCD File
C [auth A]
D [auth A]
E [auth A]
F [auth A]
G [auth A]
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A],
J [auth B],
K [auth B],
L [auth B],
M [auth B],
N [auth B]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.91 Å
  • R-Value Free:  0.277 (Depositor), 0.276 (DCC) 
  • R-Value Work:  0.230 (Depositor), 0.225 (DCC) 
  • R-Value Observed: 0.232 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 77.282α = 90
b = 59.906β = 102.63
c = 119.932γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
PHASERphasing
PHENIXrefinement
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2013-10-30
    Type: Initial release
  • Version 1.1: 2015-06-17
    Changes: Database references
  • Version 1.2: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Database references, Derived calculations, Structure summary
  • Version 1.3: 2023-11-08
    Changes: Data collection, Database references, Refinement description, Structure summary
  • Version 1.4: 2024-11-06
    Changes: Structure summary