3M7O | pdb_00003m7o

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 (Depositor), 0.229 (DCC) 
  • R-Value Work: 
    0.195 (Depositor), 0.196 (DCC) 
  • R-Value Observed: 
    0.196 (Depositor) 

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Literature

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

Harada, H., Ohto, U., Satow, Y.

(2010) J Mol Biology 400: 838-846

  • DOI: https://doi.org/10.1016/j.jmb.2010.05.063
  • Primary Citation 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. 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.

Macromolecule Content 

  • Total Structure Weight: 76.57 kDa 
  • Atom Count: 4,955 
  • Modeled Residue Count: 530 
  • Deposited Residue Count: 648 
  • Unique protein chains: 1

Macromolecules

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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Lymphocyte antigen 86
A, B, C, D
162Mus musculusMutation(s): 0 
Gene Names: Ly86, Md1
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
Glycosylation
Glycosylation Sites: 2
Go to GlyGen: O88188-1
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / 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
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
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

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free:  0.227 (Depositor), 0.229 (DCC) 
  • R-Value Work:  0.195 (Depositor), 0.196 (DCC) 
  • R-Value Observed: 0.196 (Depositor) 
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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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
  • Version 2.1: 2024-10-16
    Changes: Data collection, Database references, Structure summary