3M7O

Crystal structure of mouse MD-1 in complex with phosphatidylcholine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.196 

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Ligand Structure Quality Assessment 


This is version 2.0 of the entry. See complete history


Literature

Crystal structure of mouse MD-1 with endogenous phospholipid bound in its cavity

Harada, H.Ohto, U.Satow, Y.

(2010) J Mol Biol 400: 838-846

  • DOI: 10.1016/j.jmb.2010.05.063
  • Primary Citation of Related Structures:  
    3M7O

  • PubMed Abstract: 
  • MD-1 is a glycoprotein that associates with a B-cell-specific RP105 protein and has a low sequence identity of 16% to MD-2 that associates with Toll-like receptor 4 and recognizes endotoxic lipopolysaccharide. MD-1 and RP105 are supposed to mediate lipopolysaccharide recognition; however, little is known about their structures and functions ...

    MD-1 is a glycoprotein that associates with a B-cell-specific RP105 protein and has a low sequence identity of 16% to MD-2 that associates with Toll-like receptor 4 and recognizes endotoxic lipopolysaccharide. MD-1 and RP105 are supposed to mediate lipopolysaccharide recognition; however, little is known about their structures and functions. Here, the crystal structure of mouse MD-1 is determined at 1.65 A resolution. MD-1 has a hydrophobic cavity sandwiched by two beta-sheets as is MD-2. The cavity is 25 A long, 5 A wide, and 10 A deep: longer, narrower, and shallower than that of MD-2. No charged residues are located on the cavity entrance. MD-1 is primarily monomeric in solution but shows a dimeric assembly in the crystal lattices, with their cavity entrances facing each other. In the cavity, electron densities attributable to phosphatidylcholine are located. Together with the binding assay with tetra-acylated lipid IVa, MD-1 is shown to be a lipid-binding coreceptor.


    Organizational Affiliation

    Graduate School of Pharmaceutical Sciences, University of Tokyo, Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Lymphocyte antigen 86A, B, C, D162Mus musculusMutation(s): 0 
Gene Names: Ly86Md1
UniProt & NIH Common Fund Data Resources
Find proteins for O88188 (Mus musculus)
Explore O88188 
Go to UniProtKB:  O88188
IMPC:  MGI:1321404
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO88188
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
L9R
Query on L9R

Download Ideal Coordinates CCD File 
G [auth A],
Y [auth D]
(2S)-3-(octadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate
C44 H86 N O8 P
ATHVAWFAEPLPPQ-FLHXZNPISA-N
 Ligand Interaction
NAG
Query on NAG

Download Ideal Coordinates CCD File 
E [auth A],
F [auth A],
M [auth B],
N [auth B],
R [auth C],
E [auth A],
F [auth A],
M [auth B],
N [auth B],
R [auth C],
S [auth C],
W [auth D],
X [auth D]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
BEN
Query on BEN

Download Ideal Coordinates CCD File 
AA [auth D],
BA [auth D],
CA [auth D],
DA [auth D],
H [auth A],
AA [auth D],
BA [auth D],
CA [auth D],
DA [auth D],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
O [auth B],
P [auth B],
Q [auth B],
T [auth C],
U [auth C],
V [auth C],
Z [auth D]
BENZAMIDINE
C7 H8 N2
PXXJHWLDUBFPOL-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.196 
  • Space Group: P 43
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 90.299α = 90
b = 90.299β = 90
c = 86.714γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
autoSHARPphasing
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
  • Version 1.2: 2014-01-22
    Changes: Database references
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary