1FNE

HISTOCOMPATIBILITY ANTIGEN

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.231 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history. 

Literature

Structural and functional consequences of altering a peptide MHC anchor residue.

Kersh, G.J., Miley, M.J., Nelson, C.A., Grakoui, A., Horvath, S., Donermeyer, D.L., Kappler, J., Allen, P.M., Fremont, D.H.

(2001) J.Immunol. 166: 3345-3354

  • DOI: 10.4049/jimmunol.166.5.3345
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    • To better understand TCR discrimination of multiple ligands, we have analyzed the crystal structures of two Hb peptide/I-E(k) complexes that differ by only a single amino acid substitution at the P6 anchor position within the peptide (E73D). Detailed ...

    To better understand TCR discrimination of multiple ligands, we have analyzed the crystal structures of two Hb peptide/I-E(k) complexes that differ by only a single amino acid substitution at the P6 anchor position within the peptide (E73D). Detailed comparison of multiple independently determined structures at 1.9 A resolution reveals that removal of a single buried methylene group can alter a critical portion of the TCR recognition surface. Significant variance was observed in the peptide P5-P8 main chain as well as a rotamer difference at LeuP8, approximately 10 A distal from the substitution. No significant variations were observed in the conformation of the two MHC class II molecules. The ligand alteration results in two peptide/MHC complexes that generate bulk T cell responses that are distinct and essentially nonoverlapping. For the Hb-specific T cell 3.L2, substitution reduces the potency of the ligand 1000-fold. Soluble 3.L2 TCR binds the two peptide/MHC complexes with similar affinity, although with faster kinetics. These results highlight the role of subtle variations in MHC Ag presentation on T cell activation and signaling.

    Organizational Affiliation: 

    Department of Pathology and Center for Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (MHC CLASS II I-EK, ALPHA CHAIN)
A, C
192Mus musculusMutation(s): 0 
Find proteins for P04224 (Mus musculus)
Go to UniProtKB:  P04224
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (MHC CLASS II I-EK, BETA CHAIN)
B, D
224Mus musculusMutation(s): 1 
Gene Names: Hbb-b2
Find proteins for P02089 (Mus musculus)
Go to UniProtKB:  P02089
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG
Download SDF File 
Download CCD File 
A, B, C, D
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.231 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 146.900α = 90.00
b = 56.853β = 91.76
c = 116.726γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2001-03-07
    Type: Initial release
  • Version 1.1: 2007-10-16
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance
  • Version 1.3: 2017-08-23
    Type: Advisory, Refinement description, Source and taxonomy
  • Version 1.4: 2018-03-14
    Type: Database references