5KD4

Crystal Structure of Murine MHC-I H-2Dd in complex with Murine Beta2-Microglobulin and a Variant of Peptide (PVI10) of HIV gp120 MN Isolate (IGPGRAFYVI)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.05 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.184 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Effects of Cross-Presentation, Antigen Processing, and Peptide Binding in HIV Evasion of T Cell Immunity.

Frey, B.F.Jiang, J.Sui, Y.Boyd, L.F.Yu, B.Tatsuno, G.Billeskov, R.Solaymani-Mohammadi, S.Berman, P.W.Margulies, D.H.Berzofsky, J.A.

(2018) J. Immunol. 200: 1853-1864

  • DOI: 10.4049/jimmunol.1701523
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Unlike cytosolic processing and presentation of viral Ags by virus-infected cells, Ags first expressed in infected nonprofessional APCs, such as CD4 <sup>+ </sup> T cells in the case of HIV, are taken up by dendritic cells and cross-presented. This g ...

    Unlike cytosolic processing and presentation of viral Ags by virus-infected cells, Ags first expressed in infected nonprofessional APCs, such as CD4 + T cells in the case of HIV, are taken up by dendritic cells and cross-presented. This generally requires entry through the endocytic pathway, where endosomal proteases have first access for processing. Thus, understanding virus escape during cross-presentation requires an understanding of resistance to endosomal proteases, such as cathepsin S (CatS). We have modified HIV-1 MN gp120 by mutating a key CatS cleavage site (Thr 322 Thr 323 ) in the V3 loop of the immunodominant epitope IGPGRAFY TT to IGPGRAFY VV to prevent digestion. We found this mutation to facilitate cross-presentation and provide evidence from MHC binding and X-ray crystallographic structural studies that this results from preservation of the epitope rather than an increased epitope affinity for the MHC class I molecule. In contrast, when the protein is expressed by a vaccinia virus in the cytosol, the wild-type protein is immunogenic without this mutation. These proof-of-concept results show that a virus like HIV, infecting predominantly nonprofessional presenting cells, can escape T cell recognition by incorporating a CatS cleavage site that leads to destruction of an immunodominant epitope when the Ag undergoes endosomal cross-presentation.


    Organizational Affiliation

    Molecular Biology Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892; and.,Vaccine Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892; suiy@mail.nih.gov.,Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA 95064.,Vaccine Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
H-2 class I histocompatibility antigen, D-D alpha chain
A, C
277Mus musculusMutation(s): 0 
Gene Names: H2-D1
Find proteins for P01900 (Mus musculus)
Go to UniProtKB:  P01900
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Beta-2-microglobulin
B, D
100Mus musculusMutation(s): 0 
Gene Names: B2m
Find proteins for P01887 (Mus musculus)
Go to UniProtKB:  P01887
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Peptide of HIV gp120 MN isolate, PVI10 (IGPGRAFYVI)
P, Q
10Human immunodeficiency virus type 1 group M subtype B (isolate MN)Mutation(s): 0 
Gene Names: env
Find proteins for P05877 (Human immunodeficiency virus type 1 group M subtype B (isolate MN))
Go to UniProtKB:  P05877
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.05 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.184 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 47.130α = 90.00
b = 90.300β = 113.19
c = 120.070γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
XDSdata scaling
XDSdata reduction
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-10-11
    Type: Initial release
  • Version 1.1: 2018-02-07
    Type: Database references
  • Version 1.2: 2018-02-28
    Type: Database references