2VE6

Crystal structure of a Murine MHC class I H2-Db molecule in complex with a photocleavable peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.291 
  • R-Value Work: 0.234 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Discovery of Cd8+ T Cell Epitopes in Chlamydia Trachomatis Infection Through Use of Caged Class I Mhc Tetramers.

Grotenbreg, G.M.Roan, N.R.Guillen, E.Meijers, R.Wang, J.H.Bell, G.W.Starnbach, M.N.Ploegh, H.L.

(2008) Proc.Natl.Acad.Sci.USA 105: 3831

  • DOI: 10.1073/pnas.0711504105

  • PubMed Abstract: 
  • Class I MHC tetramers allow direct phenotypic identification of CD8(+) T cell populations, but their production remains laborious. A peptide exchange strategy that employs class I MHC products loaded with conditional ligands (caged MHC molecules) pro ...

    Class I MHC tetramers allow direct phenotypic identification of CD8(+) T cell populations, but their production remains laborious. A peptide exchange strategy that employs class I MHC products loaded with conditional ligands (caged MHC molecules) provides a fast and straightforward method to obtain diverse arrays of class I MHC tetramers and facilitates CD8(+) T cell epitope discovery. Here, we describe the development of photocleavable analogs of the FAPGNYPAL (SV9) epitope that bind H-2K(b) and H-2D(b) with full retention of their structural and functional integrity. We ranked all possible H-2K(b) octameric and H-2D(b) nonameric epitopes that span the genome of Chlamydia trachomatis and prepared MHC tetramers from approximately 2,000 of the highest scoring peptides by replacement of the SV9 analog with the peptide of choice. The resulting 2,000-member class I MHC tetramer array allowed the discovery of two variants of an epitope derived from polymorphic membrane protein I (PmpI) and an assessment of the kinetics of emergence and the effector function of the corresponding CD8(+) T cells.


    Organizational Affiliation

    Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02139, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
H-2 CLASS I HISTOCOMPATIBILITY ANTIGEN D-B ALPHA CHAIN
A, D, G, J
277Mus musculusMutation(s): 0 
Gene Names: H2-D1
Find proteins for P01899 (Mus musculus)
Go to UniProtKB:  P01899
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
BETA-2-MICROGLOBULIN
B, E, H, K
99Mus musculusMutation(s): 0 
Gene Names: B2m
Find proteins for P01887 (Mus musculus)
Go to UniProtKB:  P01887
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
SENDAI VIRUS EPITOPE RESIDUES 324-332 MODIFIED AT P7
C, F, I, L
9N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
PRQ
Query on PRQ
C, F, I, L
L-peptide linkingC9 H10 N2 O4

--

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.291 
  • R-Value Work: 0.234 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 52.240α = 90.00
b = 103.870β = 90.83
c = 168.810γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
REFMACrefinement
MOLREPphasing
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-01-22
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Version format compliance