4I0P

HLA-DO in complex with HLA-DM


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.188 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

HLA-DO acts as a substrate mimic to inhibit HLA-DM by a competitive mechanism.

Guce, A.I.Mortimer, S.E.Yoon, T.Painter, C.A.Jiang, W.Mellins, E.D.Stern, L.J.

(2013) Nat.Struct.Mol.Biol. 20: 90-98

  • DOI: 10.1038/nsmb.2460

  • PubMed Abstract: 
  • Mammalian class II major histocompatibility (MHCII) proteins bind peptide antigens in endosomal compartments of antigen-presenting cells. The nonclassical MHCII protein HLA-DM chaperones peptide-free MHCII, protecting it against inactivation, and cat ...

    Mammalian class II major histocompatibility (MHCII) proteins bind peptide antigens in endosomal compartments of antigen-presenting cells. The nonclassical MHCII protein HLA-DM chaperones peptide-free MHCII, protecting it against inactivation, and catalyzes peptide exchange on loaded MHCII. Another nonclassical MHCII protein, HLA-DO, binds HLA-DM and influences the repertoire of peptides presented by MHCII proteins. However, the mechanism by which HLA-DO functions is unclear. Here we have used X-ray crystallography, enzyme kinetics and mutagenesis approaches to investigate human HLA-DO structure and function. In complex with HLA-DM, HLA-DO adopts a classical MHCII structure, with alterations near the α subunit's 3₁₀ helix. HLA-DO binds to HLA-DM at the same sites implicated in MHCII interaction, and kinetic analysis showed that HLA-DO acts as a competitive inhibitor. These results show that HLA-DO inhibits HLA-DM function by acting as a substrate mimic, and the findings also limit the possible functional roles for HLA-DO in antigen presentation.


    Organizational Affiliation

    Department of Pathology, University of Massachusetts Medical School, Worcester, Massachusetts, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HLA-DMA protein
A, E
188Homo sapiensMutation(s): 0 
Gene Names: HLA-DMA
Find proteins for Q6ICR9 (Homo sapiens)
Go to Gene View: HLA-DMA
Go to UniProtKB:  Q6ICR9
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
HLA class II histocompatibility antigen, DM beta chain
B, F
191Homo sapiensMutation(s): 0 
Gene Names: HLA-DMB (DMB, RING7)
Find proteins for P28068 (Homo sapiens)
Go to Gene View: HLA-DMB
Go to UniProtKB:  P28068
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
HLA class II histocompatibility antigen, DO alpha chain
C, G
181Homo sapiensMutation(s): 0 
Gene Names: HLA-DOA (HLA-DNA, HLA-DZA)
Find proteins for P06340 (Homo sapiens)
Go to Gene View: HLA-DOA
Go to UniProtKB:  P06340
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
HLA class II histocompatibility antigen, DO beta chain
D, H
189Homo sapiensMutation(s): 0 
Gene Names: HLA-DOB
Find proteins for P13765 (Homo sapiens)
Go to Gene View: HLA-DOB
Go to UniProtKB:  P13765
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ACT
Query on ACT

Download SDF File 
Download CCD File 
H
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
GOL
Query on GOL

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Download CCD File 
D, F, H
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
PGE
Query on PGE

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Download CCD File 
H
TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
 Ligand Interaction
NAG
Query on NAG

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Download CCD File 
A, C, D, E, G, H
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.188 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 83.260α = 90.00
b = 147.100β = 106.49
c = 95.959γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHENIXrefinement
HKL-2000data collection
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-12-26
    Type: Initial release
  • Version 1.1: 2013-01-16
    Type: Database references