1XZ0

Crystal structure of CD1a in complex with a synthetic mycobactin lipopeptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.217 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Molecular Mechanism of Lipopeptide Presentation by CD1a.

Zajonc, D.M.Crispin, M.D.Bowden, T.A.Young, D.C.Cheng, T.Y.Hu, J.Costello, C.E.Rudd, P.M.Dwek, R.A.Miller, M.J.Brenner, M.B.Moody, D.B.Wilson, I.A.

(2005) Immunity 22: 209-219

  • DOI: 10.1016/j.immuni.2004.12.009

  • PubMed Abstract: 
  • CD1a is expressed on Langerhans cells (LCs) and dendritic cells (DCs), where it mediates T cell recognition of glycolipid and lipopeptide antigens that contain either one or two alkyl chains. We demonstrate here that CD1a-restricted T cells can discr ...

    CD1a is expressed on Langerhans cells (LCs) and dendritic cells (DCs), where it mediates T cell recognition of glycolipid and lipopeptide antigens that contain either one or two alkyl chains. We demonstrate here that CD1a-restricted T cells can discriminate the peptide component of didehydroxymycobactin lipopeptides. Structure analysis of CD1a cocrystallized with a synthetic mycobactin lipopeptide at 2.8 A resolution further reveals that the single alkyl chain is inserted deep within the A' pocket of the groove, whereas its two peptidic branches protrude along the F' pocket to the outer, alpha-helical surface of CD1a for recognition by the TCR. Remarkably, the cyclized lysine branch of the peptide moiety lies in the shallow F' pocket in a conformation that closely mimics that of the alkyl chain in the CD1a-sulfatide structure. Thus, this structural study illustrates how a single chain lipid can be presented by CD1 and that the peptide moiety of the lipopeptide is recognized by the TCR.


    Organizational Affiliation

    Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
T-cell surface glycoprotein CD1a
A, C
279Homo sapiensMutation(s): 0 
Gene Names: CD1A
Find proteins for P06126 (Homo sapiens)
Go to Gene View: CD1A
Go to UniProtKB:  P06126
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Beta-2-microglobulin
B, D
99Homo sapiensMutation(s): 0 
Gene Names: B2M
Find proteins for P61769 (Homo sapiens)
Go to Gene View: B2M
Go to UniProtKB:  P61769
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
JH0
Query on JH0

Download SDF File 
Download CCD File 
A, C
6-(HYDROXY-HEXADECANOYL-AMINO)-2-{[(4S)-2-(2-HYDROXY-PHENYL)-4,5-DIHYDRO-OXAZOLE-4-CARBONYL]-AMINO}-HEXANOIC ACID 2-[(3S)-1-(TERT-BUTYL-DIPHENYL-SILANYLOXY)-2-OXO-AZEPAN-3-YLCARBAMOYL]-(1S)-1-METHYL-ETHYL ESTER
C58 H85 N5 O10 Si
MGCJGTIHSOOPSW-SFNGQXEQSA-N
 Ligand Interaction
FUC
Query on FUC

Download SDF File 
Download CCD File 
A, C
ALPHA-L-FUCOSE
C6 H12 O5
SHZGCJCMOBCMKK-SXUWKVJYSA-N
 Ligand Interaction
NAG
Query on NAG

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.217 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 55.961α = 90.00
b = 43.235β = 91.04
c = 209.944γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
MOLREPphasing
SCALEPACKdata scaling
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-03-01
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Advisory, Version format compliance