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 sapiensMutation(s): 0 
Gene 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 sapiensMutation(s): 0 
Gene 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 sapiensMutation(s): 0 
Gene 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


View more in-depth experimental data

Entry History 

Deposition Data

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

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