1MUJ

Crystal structure of murine class II MHC I-Ab in complex with a human CLIP peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.220 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structure of MHC class II I-Ab in complex with a human CLIP peptide: Prediction of an I-Ab peptide-binding motif

Zhu, Y.Rudensky, A.Y.Teyton, A.L.Wilson, I.A.

(2003) J.Mol.Biol. 326: 1157-1174


  • PubMed Abstract: 
  • Association between the class II major histocompatibility complex (MHC) and the class II invariant chain-associated peptide (CLIP) occurs naturally as an intermediate step in the MHC class II processing pathway. Here, we report the crystal structure ...

    Association between the class II major histocompatibility complex (MHC) and the class II invariant chain-associated peptide (CLIP) occurs naturally as an intermediate step in the MHC class II processing pathway. Here, we report the crystal structure of the murine class II MHC molecule I-A(b) in complex with human CLIP at 2.15A resolution. The structure of I-A(b) accounts, via the peptide-binding groove's unique physicochemistry, for the distinct peptide repertoire bound by this allele. CLIP adopts a similar conformation to peptides bound by other I-A alleles, reinforcing the notion that CLIP is presented as a conventional peptide antigen. When compared to the related HLA-DR3/CLIP complex structure, the CLIP peptide displays a slightly different conformation and distinct interaction pattern with residues in I-A(b). In addition, after examining the published sequences of peptides presented by I-A(b), we discuss the possibility of predicting peptide alignment in the I-A(b) binding groove using a simple scoring matrix.


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
H-2 CLASS II HISTOCOMPATIBILITY ANTIGEN, A-B ALPHA CHAIN
A
190Mus musculusGene Names: H2-Aa
Find proteins for P14434 (Mus musculus)
Go to UniProtKB:  P14434
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
H-2 CLASS II HISTOCOMPATIBILITY ANTIGEN, A BETA CHAIN
B
197Mus musculusGene Names: H2-Ab1 (H2-iabeta)
Find proteins for P14483 (Mus musculus)
Go to UniProtKB:  P14483
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
CLIP peptide
C
36Homo sapiensGene Names: CD74 (DHLAG)
Find proteins for P04233 (Homo sapiens)
Go to Gene View: CD74
Go to UniProtKB:  P04233
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.220 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 63.647α = 90.00
b = 88.065β = 92.48
c = 83.740γ = 90.00
Software Package:
Software NamePurpose
MOLREPphasing
CNSrefinement
SCALEPACKdata scaling
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2002-09-23 
  • Released Date: 2003-02-18 
  • Deposition Author(s): Zhu, Y., Wilson, I.A.

Revision History 

  • Version 1.0: 2003-02-18
    Type: Initial release
  • Version 1.1: 2008-04-28
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Non-polymer description, Version format compliance