8VSP

Cryo-EM structure of human invariant chain in complex with HLA-DQ


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.12 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

Structural insights into human MHC-II association with invariant chain.

Wang, N.Waghray, D.Caveney, N.A.Jude, K.M.Garcia, K.C.

(2024) Proc Natl Acad Sci U S A 121: e2403031121-e2403031121

  • DOI: https://doi.org/10.1073/pnas.2403031121
  • Primary Citation of Related Structures:  
    8VRW, 8VSP

  • PubMed Abstract: 

    The loading of processed peptides on to major histocompatibility complex II (MHC-II) molecules for recognition by T cells is vital to cell-mediated adaptive immunity. As part of this process, MHC-II associates with the invariant chain (Ii) during biosynthesis in the endoplasmic reticulum to prevent premature peptide loading and to serve as a scaffold for subsequent proteolytic processing into MHC-II-CLIP. Cryo-electron microscopy structures of full-length Human Leukocyte Antigen-DR (HLA-DR) and HLA-DQ complexes associated with Ii, resolved at 3.0 to 3.1 Å, elucidate the trimeric assembly of the HLA/Ii complex and define atomic-level interactions between HLA, Ii transmembrane domains, loop domains, and class II-associated invariant chain peptides (CLIP). Together with previous structures of MHC-II peptide loading intermediates DO and DM, our findings complete the structural path governing class II antigen presentation.


  • Organizational Affiliation

    Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
HLA class II histocompatibility antigen, DQ alpha 1 chain
A, D, G
288Homo sapiensMutation(s): 0 
Gene Names: HLA-DQA1
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P01909 (Homo sapiens)
Explore P01909 
Go to UniProtKB:  P01909
PHAROS:  P01909
GTEx:  ENSG00000196735 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01909
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
HLA class II histocompatibility antigen, DQ beta 1 chain
B, E, H
295Homo sapiensMutation(s): 0 
Gene Names: HLA-DQB1HLA-DQB
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P01920 (Homo sapiens)
Explore P01920 
Go to UniProtKB:  P01920
PHAROS:  P01920
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01920
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
HLA class II histocompatibility antigen gamma chain
C, F, I
308Homo sapiensMutation(s): 0 
Gene Names: CD74DHLAG
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P04233 (Homo sapiens)
Explore P04233 
Go to UniProtKB:  P04233
PHAROS:  P04233
GTEx:  ENSG00000019582 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP04233
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.12 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesNIH R01 AI103867

Revision History  (Full details and data files)

  • Version 1.0: 2024-05-08
    Type: Initial release
  • Version 1.1: 2024-05-15
    Changes: Database references