1SJH

HLA-DR1 complexed with a 13 residue HIV capsid peptide

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.220 
  • R-Value Observed: 0.220 

wwPDB Validation   3D Report Full Report


This is version 1.6 of the entry. See complete history. 


Literature

A hairpin turn in a class II MHC-bound peptide orients residues outside the binding groove for T cell recognition.

Zavala-Ruiz, Z., Strug, I., Walker, B.D., Norris, P.J., Stern, L.J.

(2004) Proc Natl Acad Sci U S A 101: 13279-13284

  • DOI: 10.1073/pnas.0403371101
  • Primary Citation of Related Structures:  
    1SJE, 1SJH

  • PubMed Abstract: 

    • T cells generally recognize peptide antigens bound to MHC proteins through contacts with residues found within or immediately flanking the seven- to nine-residue sequence accommodated in the MHC peptide-binding groove. However, some T cells require peptide residues outside this region for activation, the structural basis for which is unknown ...

    T cells generally recognize peptide antigens bound to MHC proteins through contacts with residues found within or immediately flanking the seven- to nine-residue sequence accommodated in the MHC peptide-binding groove. However, some T cells require peptide residues outside this region for activation, the structural basis for which is unknown. Here, we have investigated a HIV Gag-specific T cell clone that requires an unusually long peptide antigen for activation. The crystal structure of a minimally antigenic 16-mer bound to HLA-DR1 shows that the peptide C-terminal region bends sharply into a hairpin turn as it exits the binding site, orienting peptide residues outside the MHC-binding region in position to interact with a T cell receptor. Peptide truncation and substitution studies show that both the hairpin turn and the extreme C-terminal residues are required for T cell activation. These results demonstrate a previously unrecognized mode of MHC-peptide-T cell receptor interaction.

    Organizational Affiliation: 

    Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
HLA class II histocompatibility antigen, DR alpha chainA180Homo sapiensMutation(s): 0 
Gene Names: HLA-DRA, HLA-DRA1
UniProt & NIH Common Fund Data Resources
Find proteins for P01903 (Homo sapiens)
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PHAROS:  P01903
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UniProt GroupP01903
Protein Feature View
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
HLA class II histocompatibility antigen, DRB1-1 beta chainB190Homo sapiensMutation(s): 0 
Gene Names: HLA-DRB1
UniProt & NIH Common Fund Data Resources
Find proteins for P01911 (Homo sapiens)
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PHAROS:  P01911
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UniProt GroupP01911
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
GAG polyproteinC13synthetic constructMutation(s): 0 
UniProt
Find proteins for P12495 (Human immunodeficiency virus type 1 group M subtype D (isolate Z2/CDC-Z34))
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Enterotoxin type C-3D239Staphylococcus aureusMutation(s): 4 
Gene Names: entC3, SAV2009, SA1817
UniProt
Find proteins for P0A0L5 (Staphylococcus aureus)
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UniProt GroupP0A0L5
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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.220 
  • R-Value Observed: 0.220 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 172.464α = 90
b = 172.464β = 90
c = 121.461γ = 120
Software Package:
Software NamePurpose
SCALEPACKdata scaling
AMoREphasing
CNSrefinement

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-08-17
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-11
    Changes: Refinement description
  • Version 1.4: 2018-04-04
    Changes: Data collection
  • Version 1.5: 2020-02-05
    Changes: Derived calculations, Source and taxonomy
  • Version 1.6: 2021-10-27
    Changes: Database references