3LQZ

Crystal Structure of HLA-DP2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.25 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.219 

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This is version 2.0 of the entry. See complete history


Literature

Crystal structure of HLA-DP2 and implications for chronic beryllium disease.

Dai, S.Murphy, G.A.Crawford, F.Mack, D.G.Falta, M.T.Marrack, P.Kappler, J.W.Fontenot, A.P.

(2010) Proc Natl Acad Sci U S A 107: 7425-7430

  • DOI: 10.1073/pnas.1001772107
  • Primary Citation of Related Structures:  
    3LQZ

  • PubMed Abstract: 
  • Chronic beryllium disease (CBD) is a fibrotic lung disorder caused by beryllium (Be) exposure and is characterized by granulomatous inflammation and the accumulation of Be-responsive CD4(+) T cells in the lung. Genetic susceptibility to CBD has been associated with certain alleles of the MHCII molecule HLA-DP, especially HLA-DPB1*0201 and other alleles that contain a glutamic acid residue at position 69 of the beta-chain (betaGlu69) ...

    Chronic beryllium disease (CBD) is a fibrotic lung disorder caused by beryllium (Be) exposure and is characterized by granulomatous inflammation and the accumulation of Be-responsive CD4(+) T cells in the lung. Genetic susceptibility to CBD has been associated with certain alleles of the MHCII molecule HLA-DP, especially HLA-DPB1*0201 and other alleles that contain a glutamic acid residue at position 69 of the beta-chain (betaGlu69). The HLA-DP alleles that can present Be to T cells match those implicated in the genetic susceptibility, suggesting that the HLA contribution to disease is based on the ability of those molecules to bind and present Be to T cells. The structure of HLA-DP2 and its interaction with Be are unknown. Here, we present the HLA-DP2 structure with its antigen-binding groove occupied by a self-peptide derived from the HLA-DR alpha-chain. The most striking feature of the structure is an unusual solvent exposed acidic pocket formed between the peptide backbone and the HLA-DP2 beta-chain alpha-helix and containing three glutamic acids from the beta-chain, including betaGlu69. In the crystal packing, this pocket has been filled with the guanidinium group of an arginine from a neighboring molecule. This positively charged moiety forms an extensive H-bond/salt bridge network with the three glutamic acids, offering a plausible model for how Be-containing complexes might occupy this site. This idea is strengthened by the demonstration that mutation of any of the three glutamic acids in this pocket results in loss of the ability of DP2 to present Be to T cells.


    Organizational Affiliation

    Howard Hughes Medical Institute and National Jewish Health, Denver, CO 80206, USA. dais@njhealth.org



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
HLA class II histocompatibility antigen, DP alpha 1 chainA181Homo sapiensMutation(s): 0 
Gene Names: HLA-DP1AHLA-DPA1HLA-DPA1*0103HLASB
UniProt & NIH Common Fund Data Resources
Find proteins for P20036 (Homo sapiens)
Explore P20036 
Go to UniProtKB:  P20036
PHAROS:  P20036
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
HLA-DP2 beta chain linked with DRa peptideB212Homo sapiensMutation(s): 0 
Gene Names: DAMA-245O6.7-001HLA-DPB1HLA-DPB1*0201HLA-DP1B
UniProt & NIH Common Fund Data Resources
Find proteins for P04440 (Homo sapiens)
Explore P04440 
Go to UniProtKB:  P04440
PHAROS:  P04440
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG (Subject of Investigation/LOI)
Query on NAG

Download Ideal Coordinates CCD File 
C [auth A], D [auth A], E [auth B]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.25 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.219 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 157.2823α = 90
b = 157.2823β = 90
c = 61.8048γ = 120
Software Package:
Software NamePurpose
HKL-2000data collection
PHASERphasing
REFMACrefinement
HKL-2000data reduction
SCALAdata scaling

Structure Validation

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Entry History 

Deposition Data

  • Deposited Date: 2010-02-10 
  • Released Date: 2010-04-14 
  • Deposition Author(s): Dai, S.

Revision History  (Full details and data files)

  • Version 1.0: 2010-04-14
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Refinement description, Version format compliance
  • Version 1.2: 2019-09-04
    Changes: Data collection, Derived calculations, Other
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary