9A0U | pdb_00009a0u

Docking model of HLA class I with HLA class II


Integrative Structure Snapshot

  • Multi-Scale: No 
  • Multi-State: Yes 
  • Ordered-State: No 
  • Deposited Models: 2 
  • Representative Model: 1 

This is version 1.0 of the entry. See complete history


Literature

Extracellular crosslinking mass spectrometry reveals HLA class I - HLA class II interactions on the cell surface

Armony GHeck AJRWu W

(2021) Mol Immunol 136: 16-25

  • DOI: https://doi.org/10.1016/j.molimm.2021.05.010
  • Primary Citation of Related Structures:  
    9A0U

  • PubMed Abstract: 

    Human Leukocyte Antigen (HLA) complexes are critical cell-surface protein assemblies that facilitate T-cell surveillance of almost all cell types in the body. While T-cell receptor binding to HLA class I and class II complexes is well-described with detailed structural information, the nature of cis HLA interactions within the plasma membrane of the surveyed cells remains to be better characterized, as protein-protein interactions in the membrane environment are technically challenging to profile. Here we performed extracellular chemical crosslinking on intact antigen presenting cells to specifically elucidate protein-protein interactions present in the external plasma membrane. We found that the crosslink dataset was dominated by inter- and intra-protein crosslinks involving HLA molecules, which enabled not only the construction of an HLA-centric plasma membrane protein interaction map, but also revealed multiple modes of HLA class I - HLA class II interactions with further structural modeling based on crosslinker distance restraints. Collectively, our data demonstrate that HLA molecules colocalize and can be densely packed on the plasma membrane.


  • Organizational Affiliation
    • Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands; Netherlands Proteomics Centre, Padualaan 8, 3584 CH, Utrecht, The Netherlands. Electronic address: g.armony@uu.nl.

Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
CLASS I HISTOCOMPATIBILITY ANTIGEN (HLA-A*0201) (ALPHA CHAIN)275Homo sapiensMutation(s): 19 
Gene Names: HLA-A
UniProt & NIH Common Fund Data Resources
Find proteins for P04439 (Homo sapiens)
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PHAROS:  P04439
GTEx:  ENSG00000206503 
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UniProt GroupP04439
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
BETA 2-MICROGLOBULIN100Homo sapiensMutation(s): 0 
Gene Names: B2M
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Find proteins for P61769 (Homo sapiens)
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PHAROS:  P61769
GTEx:  ENSG00000166710 
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UniProt GroupP61769
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
INFLUENZA A MATRIX PROTEIN M1 (RESIDUES 58-66)9Influenza A virus (strain A/Puerto Rico/8/1934 H1N1)Mutation(s): 0 
Gene Names: M
UniProt
Find proteins for P03485 (Influenza A virus (strain A/Puerto Rico/8/1934 H1N1))
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UniProt GroupP03485
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
HLA class II histocompatibility antigen, DR alpha chain179Homo sapiensMutation(s): 0 
Gene Names: HLA-DRA
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PHAROS:  P01903
GTEx:  ENSG00000204287 
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UniProt GroupP01903
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
HLA class II histocompatibility antigen, DRB1-4 beta chain193Homo sapiensMutation(s): 17 
Gene Names: HLA-DRB1
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PHAROS:  P01911
GTEx:  ENSG00000196126 
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UniProt GroupP01911
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Alpha-enolase14Homo sapiensMutation(s): 0 
Gene Names: ENO1
EC: 4.2.1.11
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Find proteins for P06733 (Homo sapiens)
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PHAROS:  P06733
GTEx:  ENSG00000074800 
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UniProt GroupP06733
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  • Reference Sequence

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Entity ID: 4
MoleculeChains LengthOrganismImage
GLY residue
D, H
1N/A
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Experimental Data & Validation

Integrative Structure Snapshot

  • Multi-Scale: No 
  • Multi-State: Yes 
  • Ordered-State: No 
  • Deposited Models: 2 
  • Representative Model: 1 

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-06-04
    Type: Initial release