4I0P

HLA-DO in complex with HLA-DM


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 
    0.242 (Depositor), 0.250 (DCC) 
  • R-Value Work: 
    0.188 (Depositor), 0.200 (DCC) 
  • R-Value Observed: 
    0.191 (Depositor) 

Starting Models: experimental
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Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted NAGClick on this verticalbar to view details

This is version 1.4 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: https://doi.org/10.1038/nsmb.2460
  • Primary Citation of Related Structures:  
    4I0P

  • 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 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
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
HLA-DMA protein
A, E
188Homo sapiensMutation(s): 0 
Gene Names: 3108HLA-DMA
UniProt
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Go to UniProtKB:  Q6ICR9
Entity Groups  
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UniProt GroupQ6ICR9
Glycosylation
Glycosylation Sites: 1
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
HLA class II histocompatibility antigen, DM beta chain
B, F
191Homo sapiensMutation(s): 0 
Gene Names: 3109DMBHLA-DMBRING7
UniProt & NIH Common Fund Data Resources
Find proteins for P28068 (Homo sapiens)
Explore P28068 
Go to UniProtKB:  P28068
PHAROS:  P28068
GTEx:  ENSG00000242574 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP28068
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
HLA class II histocompatibility antigen, DO alpha chain
C, G
181Homo sapiensMutation(s): 0 
Gene Names: 3111HLA-DNAHLA-DOAHLA-DZA
UniProt & NIH Common Fund Data Resources
Find proteins for P06340 (Homo sapiens)
Explore P06340 
Go to UniProtKB:  P06340
PHAROS:  P06340
GTEx:  ENSG00000204252 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP06340
Glycosylation
Glycosylation Sites: 1Go to GlyGen: P06340-1
Sequence Annotations
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
HLA class II histocompatibility antigen, DO beta chain
D, H
189Homo sapiensMutation(s): 0 
Gene Names: 3112HLA-DOB
UniProt & NIH Common Fund Data Resources
Find proteins for P13765 (Homo sapiens)
Explore P13765 
Go to UniProtKB:  P13765
PHAROS:  P13765
GTEx:  ENSG00000241106 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP13765
Glycosylation
Glycosylation Sites: 1Go to GlyGen: P13765-1
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
I [auth A]
J [auth C]
K [auth D]
M [auth E]
O [auth G]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
PGE
Query on PGE

Download Ideal Coordinates CCD File 
R [auth H]TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
L [auth D],
N [auth F],
T [auth H]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
ACT
Query on ACT

Download Ideal Coordinates CCD File 
S [auth H]ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free:  0.242 (Depositor), 0.250 (DCC) 
  • R-Value Work:  0.188 (Depositor), 0.200 (DCC) 
  • R-Value Observed: 0.191 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 83.26α = 90
b = 147.1β = 106.49
c = 95.959γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
PHASERphasing
PHENIXrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted NAGClick on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-12-26
    Type: Initial release
  • Version 1.1: 2013-01-16
    Changes: Database references
  • Version 1.2: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary
  • Version 1.3: 2023-09-20
    Changes: Data collection, Database references, Refinement description, Structure summary
  • Version 1.4: 2024-11-27
    Changes: Structure summary