7QPD

Structure of the human MHC I peptide-loading complex editing module


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.73 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Molecular basis of MHC I quality control in the peptide loading complex.

Domnick, A.Winter, C.Susac, L.Hennecke, L.Hensen, M.Zitzmann, N.Trowitzsch, S.Thomas, C.Tampe, R.

(2022) Nat Commun 13: 4701-4701

  • DOI: https://doi.org/10.1038/s41467-022-32384-z
  • Primary Citation of Related Structures:  
    7QPD

  • PubMed Abstract: 

    Major histocompatibility complex class I (MHC I) molecules are central to adaptive immunity. Their assembly, epitope selection, and antigen presentation are controlled by the MHC I glycan through a sophisticated network of chaperones and modifying enzymes. However, the mechanistic integration of the corresponding processes remains poorly understood. Here, we determine the multi-chaperone-client interaction network of the peptide loading complex (PLC) and report the PLC editing module structure by cryogenic electron microscopy at 3.7 Å resolution. Combined with epitope-proofreading studies of the PLC in near-native lipid environment, these data show that peptide-receptive MHC I molecules are stabilized by multivalent chaperone interactions including the calreticulin-engulfed mono-glucosylated MHC I glycan, which only becomes accessible for processing by α-glucosidase II upon loading of optimal epitopes. Our work reveals allosteric coupling between peptide-MHC I assembly and glycan processing. This inter-process communication defines the onset of an adaptive immune response and provides a prototypical example of the tightly coordinated events in endoplasmic reticulum quality control.


  • Organizational Affiliation

    Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438, Frankfurt am Main, Germany.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-2-microglobulinA [auth B]99Homo sapiensMutation(s): 0 
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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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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
TapasinB [auth T]428Homo sapiensMutation(s): 0 
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Find proteins for O15533 (Homo sapiens)
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PHAROS:  O15533
GTEx:  ENSG00000231925 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO15533
Glycosylation
Glycosylation Sites: 1Go to GlyGen: O15533-1
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Protein disulfide-isomerase A3C [auth E]481Homo sapiensMutation(s): 0 
EC: 5.3.4.1
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Find proteins for P30101 (Homo sapiens)
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PHAROS:  P30101
GTEx:  ENSG00000167004 
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UniProt GroupP30101
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
HLA class I histocompatibility antigen, A-3 alpha chainD [auth M]341Homo sapiensMutation(s): 0 
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Find proteins for P04439 (Homo sapiens)
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PHAROS:  P04439
GTEx:  ENSG00000206503 
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UniProt GroupP04439
Glycosylation
Glycosylation Sites: 1Go to GlyGen: P04439-1
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
CalreticulinE [auth C]400Homo sapiensMutation(s): 0 
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Find proteins for P27797 (Homo sapiens)
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PHAROS:  P27797
GTEx:  ENSG00000179218 
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UniProt GroupP27797
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  • Reference Sequence
Oligosaccharides

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Entity ID: 6
MoleculeChains Length2D Diagram Glycosylation3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseF [auth A]3N-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE
GlyCosmos:  G15407YE
GlyGen:  G15407YE
Entity ID: 7
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-D-glucopyranose-(1-3)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseG [auth D]7N-Glycosylation
Glycosylation Resources
GlyTouCan:  G85146YR
GlyCosmos:  G85146YR
GlyGen:  G85146YR
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.73 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)European UnionTA157/12-1
European Research Council (ERC)European Union789121

Revision History  (Full details and data files)

  • Version 1.0: 2022-07-20
    Type: Initial release
  • Version 1.1: 2022-08-24
    Changes: Database references