5WLG

Crystal Structure of H-2Db with the GAP501 peptide (SQL)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.220 

Starting Models: experimental
View more details

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

A T Cell Receptor Locus Harbors a Malaria-Specific Immune Response Gene.

Van Braeckel-Budimir, N.Gras, S.Ladell, K.Josephs, T.M.Pewe, L.Urban, S.L.Miners, K.L.Farenc, C.Price, D.A.Rossjohn, J.Harty, J.T.

(2017) Immunity 47: 835-847.e4

  • DOI: https://doi.org/10.1016/j.immuni.2017.10.013
  • Primary Citation of Related Structures:  
    5WLG, 5WLI

  • PubMed Abstract: 

    Immune response (Ir) genes, originally proposed by Baruj Benacerraf to explain differential antigen-specific responses in animal models, have become synonymous with the major histocompatibility complex (MHC). We discovered a non-MHC-linked Ir gene in a T cell receptor (TCR) locus that was required for CD8 + T cell responses to the Plasmodium berghei GAP50 40-48 epitope in mice expressing the MHC class I allele H-2D b . GAP50 40-48 -specific CD8 + T cell responses emerged from a very large pool of naive Vβ8.1 + precursors, which dictated susceptibility to cerebral malaria and conferred protection against recombinant Listeria monocytogenes infection. Structural analysis of a prototypical Vβ8.1 + TCR-H-2D b -GAP50 40-48 ternary complex revealed that germline-encoded complementarity-determining region 1β residues present exclusively in the Vβ8.1 segment mediated essential interactions with the GAP50 40-48 peptide. Collectively, these findings demonstrated that Vβ8.1 functioned as an Ir gene that was indispensable for immune reactivity against the malaria GAP50 40-48 epitope.


  • Organizational Affiliation

    Department of Microbiology, University of Iowa, Iowa City, IA 52242, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
H-2 class I histocompatibility antigen, D-B alpha chain
A, F
278Mus musculusMutation(s): 0 
Gene Names: H2-D1
UniProt
Find proteins for P01899 (Mus musculus)
Explore P01899 
Go to UniProtKB:  P01899
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01899
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-2-microglobulin
B, G
99Mus musculusMutation(s): 0 
Gene Names: B2m
UniProt & NIH Common Fund Data Resources
Find proteins for P01887 (Mus musculus)
Explore P01887 
Go to UniProtKB:  P01887
IMPC:  MGI:88127
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01887
Sequence Annotations
Expand
  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
GAP50 peptide
C, H
9Plasmodium bergheiMutation(s): 0 
Gene Names: GAP50PBK173_000161900PBNK65E_000154900PBNK65NY_000154100PBSP11A_000154100PBSP11RLL_000154100
UniProt
Find proteins for A0A0Y9W4B5 (Plasmodium berghei)
Explore A0A0Y9W4B5 
Go to UniProtKB:  A0A0Y9W4B5
Entity Groups  
UniProt GroupA0A0Y9W4B5
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
T cell receptor alpha variable 8D-2,Human nkt tcr alpha chain
D, I
182Mus musculusHomo sapiens
This entity is chimeric
Mutation(s): 0 
Gene Names: Trav8d-2B2MHDCMA22P
UniProt
Find proteins for K7N5M3 (Homo sapiens)
Explore K7N5M3 
Go to UniProtKB:  K7N5M3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupK7N5M3
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
T-cell receptor beta chain V region C5,Human nkt tcr beta chain
E, J
243Mus musculusHomo sapiens
This entity is chimeric
Mutation(s): 0 
UniProt
Find proteins for P04213 (Mus musculus)
Explore P04213 
Go to UniProtKB:  P04213
Find proteins for K7N5M4 (Homo sapiens)
Explore K7N5M4 
Go to UniProtKB:  K7N5M4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsK7N5M4P04213
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.220 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 115.735α = 90
b = 70.21β = 108.28
c = 116.488γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
Aimlessdata scaling
PHASERphasing
PDB_EXTRACTdata extraction
XDSdata processing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-11-15
    Type: Initial release
  • Version 1.1: 2018-11-28
    Changes: Data collection, Database references, Source and taxonomy, Structure summary
  • Version 1.2: 2019-05-29
    Changes: Data collection, Database references
  • Version 1.3: 2023-10-04
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.4: 2024-10-23
    Changes: Structure summary