4I0P | pdb_00004i0p

HLA-DO in complex with HLA-DM


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 
    0.242 (Depositor), 0.248 (DCC) 
  • R-Value Work: 
    0.188 (Depositor), 0.197 (DCC) 
  • R-Value Observed: 
    0.191 (Depositor) 

Starting Models: experimental
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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 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.

Macromolecule Content 

  • Total Structure Weight: 172.08 kDa 
  • Atom Count: 12,064 
  • Modeled Residue Count: 1,488 
  • Deposited Residue Count: 1,498 
  • Unique protein chains: 4

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
HLA-DMA protein
A, E
188Homo sapiensMutation(s): 0 
Gene Names: 3108HLA-DMA
UniProt
Find proteins for Q6ICR9 (Homo sapiens)
Explore Q6ICR9 
Go to UniProtKB:  Q6ICR9
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6ICR9
Glycosylation
Glycosylation Sites: 1
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
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
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UniProt GroupP28068
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
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: 2Go to GlyGen: P06340-1
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
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]
I [auth A],
J [auth C],
K [auth D],
M [auth E],
O [auth G],
P [auth G],
Q [auth H]
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), 0.248 (DCC) 
  • R-Value Work:  0.188 (Depositor), 0.197 (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 


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