3C5J

Crystal structure of HLA DR52c


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.202 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The structure of HLA-DR52c: comparison to other HLA-DRB3 alleles.

Dai, S.Crawford, F.Marrack, P.Kappler, J.W.

(2008) Proc.Natl.Acad.Sci.USA 105: 11893-11897

  • DOI: 10.1073/pnas.0805810105

  • PubMed Abstract: 
  • Class II major histocompatibility complex (MHCII) molecules present antigens to CD4(+) T cells. In addition to the most commonly studied human MHCII isotype, HLA-DR, whose beta chain is encoded by the HLA-DRB1 locus, several other isotypes that use t ...

    Class II major histocompatibility complex (MHCII) molecules present antigens to CD4(+) T cells. In addition to the most commonly studied human MHCII isotype, HLA-DR, whose beta chain is encoded by the HLA-DRB1 locus, several other isotypes that use the same alpha chain but have beta chains encoded by other genes. These other DR molecules also are expressed in antigen-presenting cells and are known to participate in peptide presentation to T cells and to be recognized as alloantigens by other T cells. Like some of the HLA-DRB1 alleles, several of these alternate DR molecules have been associated with specific autoimmune diseases and T cell hypersensitivity. Here we present the structure of an HLA-DR molecule (DR52c) containing one of these alternate beta chains (HLA-DRB3*0301) bound to a self-peptide derived from the Tu elongation factor. The molecule shares structurally conserved elements with other MHC class II molecules but has some unique features in the peptide-binding groove. Comparison of the three major HLA-DBR3 alleles (DR52a, b, and c) suggests that they were derived from one another by recombination events that scrambled the four major peptide-binding pockets at peptide positions 1, 4, 6, and 9 but left virtually no polymorphisms elsewhere in the molecules.


    Organizational Affiliation

    Integrated Department of Immunology, Howard Hughes Medical Institute, National Jewish Medical and Research Center, Denver, CO 80206, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HLA class II histocompatibility antigen, DR alpha chain
A
181Homo sapiensGene Names: HLA-DRA (HLA-DRA1)
Find proteins for P01903 (Homo sapiens)
Go to Gene View: HLA-DRA
Go to UniProtKB:  P01903
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
MHC class II antigen
B
190Homo sapiensGene Names: HLA-DRB3
Find proteins for B8YAC7 (Homo sapiens)
Go to Gene View: HLA-DRB3
Go to UniProtKB:  B8YAC7
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Elongation factor 1-alpha 2
C
13Homo sapiensGene Names: EEF1A2 (EEF1AL, STN)
Find proteins for Q05639 (Homo sapiens)
Go to Gene View: EEF1A2
Go to UniProtKB:  Q05639
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
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: 1.8 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.202 
  • Space Group: P 43 2 2
Unit Cell:
Length (Å)Angle (°)
a = 83.380α = 90.00
b = 83.380β = 90.00
c = 132.910γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
DENZOdata reduction
AMoREphasing
SCALEPACKdata scaling
HKL-2000data collection
PDB_EXTRACTdata extraction
CNSrefinement
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2008-01-31 
  • Released Date: 2008-08-05 
  • Deposition Author(s): Dai, S., Kappler, J.W.

Revision History 

  • Version 1.0: 2008-08-05
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Non-polymer description, Version format compliance
  • Version 1.2: 2017-10-25
    Type: Refinement description