3C5J

Crystal structure of HLA DR52c

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.202 

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This is version 1.3 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 U S A 105: 11893-11897

  • DOI: 10.1073/pnas.0805810105
  • Primary Citation of Related Structures:  
    3C5J

  • 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 the same alpha chain but have beta chains encoded by other genes ...

    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
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
HLA class II histocompatibility antigen, DR alpha chainA181Homo sapiensMutation(s): 0 
Gene Names: HLA-DRA, HLA-DRA1
UniProt & NIH Common Fund Data Resources
Find proteins for P01903 (Homo sapiens)
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PHAROS:  P01903
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UniProt GroupP01903
Protein Feature View
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
MHC class II antigenB190Homo sapiensMutation(s): 0 
Gene Names: HLA-DRB3
UniProt
Find proteins for B8YAC7 (Homo sapiens)
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Go to UniProtKB:  B8YAC7
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UniProt GroupB8YAC7
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  • Reference Sequence

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Elongation factor 1-alpha 2C13Homo sapiensMutation(s): 0 
Gene Names: EEF1A2, EEF1AL, STN
UniProt & NIH Common Fund Data Resources
Find proteins for Q05639 (Homo sapiens)
Explore Q05639 
Go to UniProtKB:  Q05639
PHAROS:  Q05639
Entity Groups  
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UniProt GroupQ05639
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG
Download Ideal Coordinates CCD File 
D [auth A],
E [auth B]		2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N		 Ligand Interaction
SO4
Query on SO4
Download Ideal Coordinates CCD File 
F [auth B]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.202 
  • Space Group: P 43 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 83.38α = 90
b = 83.38β = 90
c = 132.91γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

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

Revision History  (Full details and data files)

  • Version 1.0: 2008-08-05
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.2: 2017-10-25
    Changes: Refinement description
  • Version 1.3: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary