3OV6

CD1c in complex with MPM (mannosyl-beta1-phosphomycoketide)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.502 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.240 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The 2.5 A structure of CD1c in complex with a mycobacterial lipid reveals an open groove ideally suited for diverse antigen presentation

Scharf, L.Li, N.S.Hawk, A.J.Garzon, D.Zhang, T.Fox, L.M.Kazen, A.R.Shah, S.Haddadian, E.J.Gumperz, J.E.Saghatelian, A.Faraldo-Gomez, J.D.Meredith, S.C.Piccirilli, J.A.Adams, E.J.

(2010) Immunity 33: 853-862

  • DOI: 10.1016/j.immuni.2010.11.026

  • PubMed Abstract: 
  • CD1 molecules function to present lipid-based antigens to T cells. Here we present the crystal structure of CD1c at 2.5 Å resolution, in complex with the pathogenic Mycobacterium tuberculosis antigen mannosyl-β1-phosphomycoketide (MPM). CD1c accommod ...

    CD1 molecules function to present lipid-based antigens to T cells. Here we present the crystal structure of CD1c at 2.5 Å resolution, in complex with the pathogenic Mycobacterium tuberculosis antigen mannosyl-β1-phosphomycoketide (MPM). CD1c accommodated MPM's methylated alkyl chain exclusively in the A' pocket, aided by a unique exit portal underneath the α1 helix. Most striking was an open F' pocket architecture lacking the closed cavity structure of other CD1 molecules, reminiscent of peptide binding grooves of classical major histocompatibility complex molecules. This feature, combined with tryptophan-fluorescence quenching during loading of a dodecameric lipopeptide antigen, provides a compelling model by which both the lipid and peptide moieties of the lipopeptide are involved in CD1c presentation of lipopeptides.


    Organizational Affiliation

    Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60637, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Beta-2-microglobulin, T-cell surface glycoprotein CD1c, T-cell surface glycoprotein CD1b
A
397Homo sapiensMutation(s): 6 
Gene Names: CD1C, B2M, CD1B
Find proteins for P29017 (Homo sapiens)
Go to Gene View: CD1C
Go to UniProtKB:  P29017
Find proteins for P61769 (Homo sapiens)
Go to Gene View: B2M
Go to UniProtKB:  P61769
Find proteins for P29016 (Homo sapiens)
Go to Gene View: CD1B
Go to UniProtKB:  P29016
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
D12
Query on D12

Download SDF File 
Download CCD File 
A
DODECANE
C12 H26
SNRUBQQJIBEYMU-UHFFFAOYSA-N
 Ligand Interaction
MK0
Query on MK0

Download SDF File 
Download CCD File 
A
1-O-[(S)-hydroxy{[(4S,8S,16S,20S)-4,8,12,16,20-pentamethylheptacosyl]oxy}phosphoryl]-beta-D-mannopyranose
C38 H77 O9 P
BWDAWKXFHWFXEQ-RIEBCBCMSA-N
 Ligand Interaction
NAG
Query on NAG

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.502 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.240 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 53.724α = 90.00
b = 87.087β = 90.00
c = 88.808γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data collection
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-01-19
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2017-07-26
    Type: Advisory, Data collection, Refinement description, Source and taxonomy