4QRT

Crystal Structure of HLA B*0801 in complex with ELN_YYM, ELNRKMIYM


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.4 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.179 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Molecular imprint of exposure to naturally occurring genetic variants of human cytomegalovirus on the T cell repertoire.

Smith, C.Gras, S.Brennan, R.M.Bird, N.L.Valkenburg, S.A.Twist, K.A.Burrows, J.M.Miles, J.J.Chambers, D.Bell, S.Campbell, S.Kedzierska, K.Burrows, S.R.Rossjohn, J.Khanna, R.

(2014) Sci Rep 4: 3993-3993

  • DOI: 10.1038/srep03993
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Exposure to naturally occurring variants of herpesviruses in clinical settings can have a dramatic impact on anti-viral immunity. Here we have evaluated the molecular imprint of variant peptide-MHC complexes on the T-cell repertoire during human cyto ...

    Exposure to naturally occurring variants of herpesviruses in clinical settings can have a dramatic impact on anti-viral immunity. Here we have evaluated the molecular imprint of variant peptide-MHC complexes on the T-cell repertoire during human cytomegalovirus (CMV) infection and demonstrate that primary co-infection with genetic variants of CMV was coincident with development of strain-specific T-cell immunity followed by emergence of cross-reactive virus-specific T-cells. Cross-reactive CMV-specific T cells exhibited a highly conserved public T cell repertoire, while T cells directed towards specific genetic variants displayed oligoclonal repertoires, unique to each individual. T cell recognition foot-print and pMHC-I structural analyses revealed that the cross-reactive T cells accommodate alterations in the pMHC complex with a broader foot-print focussing on the core of the peptide epitope. These findings provide novel molecular insight into how infection with naturally occurring genetic variants of persistent human herpesviruses imprints on the evolution of the anti-viral T-cell repertoire.


    Organizational Affiliation

    QIMR Berghofer Medical Research Institute, Centre for Immunotherapy and Vaccine Development, Brisbane 4029 QLD Australia.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HLA class I histocompatibility antigen, B-8 alpha chain
A
276Homo sapiensMutation(s): 0 
Gene Names: HLA-B (HLAB)
Find proteins for P30460 (Homo sapiens)
Go to Gene View: HLA-B
Go to UniProtKB:  P30460
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Beta-2-microglobulin
B
100Homo sapiensMutation(s): 0 
Gene Names: B2M
Find proteins for P61769 (Homo sapiens)
Go to Gene View: B2M
Go to UniProtKB:  P61769
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Major immediate-early protein
C
9Human cytomegalovirusMutation(s): 0 
Find proteins for Q9YRL8 (Human cytomegalovirus)
Go to UniProtKB:  Q9YRL8
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EDO
Query on EDO

Download SDF File 
Download CCD File 
A
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.4 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.179 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 50.540α = 90.00
b = 81.580β = 90.00
c = 111.710γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
SCALAdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
XSCALEdata scaling
REFMACrefinement
Blu-Icedata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-07-16
    Type: Initial release