1G7P

CRYSTAL STRUCTURE OF MHC CLASS I H-2KB HEAVY CHAIN COMPLEXED WITH BETA-2 MICROGLOBULIN AND YEAST ALPHA-GLUCOSIDASE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.205 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structure of a non-canonical high affinity peptide complexed with MHC class I: a novel use of alternative anchors.

Apostolopoulos, V.Yu, M.Corper, A.L.Li, W.McKenzie, I.F.Teyton, L.Wilson, I.A.

(2002) J.Mol.Biol. 318: 1307-1316


  • PubMed Abstract: 
  • The crystal structure of a non-standard peptide, YEA9, in complex with H-2Kb, at 1.5 A resolution demonstrates how YEA9 peptide can bind with surprisingly high affinity through insertion of alternative, long, non-canonical anchors into the B and E po ...

    The crystal structure of a non-standard peptide, YEA9, in complex with H-2Kb, at 1.5 A resolution demonstrates how YEA9 peptide can bind with surprisingly high affinity through insertion of alternative, long, non-canonical anchors into the B and E pockets. The use of "alternative pockets" represents a new mode of high affinity peptide binding, that should be considered when predicting peptide epitopes for MHC class I. These novel interactions encountered in this non-canonical high affinity peptide-MHC complex should help predict additional binding peptides from primary protein sequences and aid in the design of alternative approaches for peptide-based vaccines.


    Organizational Affiliation

    Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA 92037, USA. v.apostolopoulos@ari.unimelb.edu.au




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
H-2 CLASS I HISTOCOMPATIBILITY ANTIGEN, K-B ALPHA CHAIN
A
274Mus musculusMutation(s): 0 
Gene Names: H2-K1 (H2-K)
Find proteins for P01901 (Mus musculus)
Go to UniProtKB:  P01901
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
BETA-2 MICROGLOBULIN
B
99Mus musculusMutation(s): 0 
Gene Names: B2m
Find proteins for P01887 (Mus musculus)
Go to UniProtKB:  P01887
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
ALPHA-GLUCOSIDASE P1
P
9Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: MAL62 (MAL6S)
EC: 3.2.1.20
Find proteins for P07265 (Saccharomyces cerevisiae)
Go to UniProtKB:  P07265
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FUC
Query on FUC

Download SDF File 
Download CCD File 
A
ALPHA-L-FUCOSE
C6 H12 O5
SHZGCJCMOBCMKK-SXUWKVJYSA-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: 1.5 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.205 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 136.090α = 90.00
b = 88.344β = 90.00
c = 45.659γ = 90.00
Software Package:
Software NamePurpose
AMoREphasing
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-07-17
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Non-polymer description, Version format compliance