3MU3

Crystal structure of chicken MD-1 complexed with lipid IVa


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.232 
  • R-Value Observed: 0.234 

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Literature

Crystal structure of soluble MD-1 and its interaction with lipid IVa.

Yoon, S.I.Hong, M.Han, G.W.Wilson, I.A.

(2010) Proc Natl Acad Sci U S A 107: 10990-10995

  • DOI: 10.1073/pnas.1004153107
  • Primary Citation of Related Structures:  
    3MTX, 3MU3

  • PubMed Abstract: 
  • Lipopolysaccharide (LPS) of Gram-negative bacteria is a common pathogen-associated molecular pattern (PAMP) that induces potent innate immune responses. The host immune response against LPS is triggered by myeloid differentiation factor 2 (MD-2) in association with Toll-like receptor 4 (TLR4) on the cell surface ...

    Lipopolysaccharide (LPS) of Gram-negative bacteria is a common pathogen-associated molecular pattern (PAMP) that induces potent innate immune responses. The host immune response against LPS is triggered by myeloid differentiation factor 2 (MD-2) in association with Toll-like receptor 4 (TLR4) on the cell surface. The MD-2/TLR4-mediated LPS response is regulated by the evolutionarily related complex of MD-1 and Toll-like receptor homolog RP105. Here, we report crystallographic and biophysical data that demonstrate a previously unidentified direct interaction of MD-1 with LPS. The crystal structure of chicken MD-1 (cMD-1) at 2.0 A resolution exhibits a beta-cup-like fold, similar to MD-2, that encloses a hydrophobic cavity between the two beta-sheets. A lipid-like moiety was observed inside the cavity, suggesting the possibility of a direct MD-1/LPS interaction. LPS was subsequently identified as an MD-1 ligand by native gel electrophoresis and gel filtration analyses. The crystal structure of cMD-1 with lipid IVa, an LPS precursor, at 2.4 A resolution revealed that the lipid inserts into the deep hydrophobic cavity of the beta-cup-like structure, but with some important differences compared with MD-2. These findings suggest that soluble MD-1 alone, in addition to its complex with RP105, can regulate host LPS sensitivity.


    Organizational Affiliation

    Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Protein MD-1A, B151Gallus gallusMutation(s): 0 
Gene Names: LY86MD-1MD1
UniProt
Find proteins for Q90890 (Gallus gallus)
Explore Q90890 
Go to UniProtKB:  Q90890
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ90890
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
LP5
Query on LP5

Download Ideal Coordinates CCD File 
D [auth A],
G [auth B]
(R)-((2R,3S,4R,5R,6R)-3-HYDROXY-2-(HYDROXYMETHYL)-5-((R)-3-HYDROXYTETRADECANAMIDO)-6-(PHOSPHONOOXY)TETRAHYDRO-2H-PYRAN-4-YL) 3-HYDROXYTETRADECANOATE
C34 H66 N O12 P
HEHQDWUWJVPREQ-XQJZMFRCSA-N
 Ligand Interaction
LP4
Query on LP4

Download Ideal Coordinates CCD File 
C [auth A],
F [auth B]
2-deoxy-3-O-[(3R)-3-hydroxytetradecanoyl]-2-{[(3R)-3-hydroxytetradecanoyl]amino}-4-O-phosphono-beta-D-glucopyranose
C34 H66 N O12 P
AJRPJFBMHCTNGK-XQJZMFRCSA-N
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
E [auth A],
H [auth B],
I [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.232 
  • R-Value Observed: 0.234 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 39.465α = 90
b = 78.15β = 90
c = 101.236γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
PHASERphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-06-09
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance