4QRP | pdb_00004qrp

Crystal Structure of HLA B*0801 in complex with HSKKKCDEL and DD31 TCR


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 
    0.248 (Depositor), 0.268 (DCC) 
  • R-Value Work: 
    0.206 (Depositor), 0.229 (DCC) 
  • R-Value Observed: 
    0.209 (Depositor) 

Starting Models: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 4QRP

This is version 1.6 of the entry. See complete history

Literature

An Extensive Antigenic Footprint Underpins Immunodominant TCR Adaptability against a Hypervariable Viral Determinant.

Nivarthi, U.K.Gras, S.Kjer-Nielsen, L.Berry, R.Lucet, I.S.Miles, J.J.Tracy, S.L.Purcell, A.W.Bowden, D.S.Hellard, M.Rossjohn, J.McCluskey, J.Bharadwaj, M.

(2014) J Immunol 193: 5402-5413

  • DOI: https://doi.org/10.4049/jimmunol.1401357
  • Primary Citation Related Structures: 
    4QRP, 4QRQ

  • PubMed Abstract: 

    Mutations in T cell epitopes are implicated in hepatitis C virus (HCV) persistence and can impinge on vaccine development. We recently demonstrated a narrow bias in the human TCR repertoire targeted at an immunodominant, but highly mutable, HLA-B*0801-restricted epitope ((1395)HSKKKCDEL(1403) [HSK]). To investigate if the narrow TCR repertoire facilitates CTL escape, structural and biophysical studies were undertaken, alongside comprehensive functional analysis of T cells targeted at the natural variants of HLA-B*0801-HSK in different HCV genotypes and quasispecies. Interestingly, within the TCR-HLA-B*0801-HSK complex, the TCR contacts all available surface-exposed residues of the HSK determinant. This broad epitope coverage facilitates cross-genotypic reactivity and recognition of common mutations reported in HCV quasispecies, albeit to a varying degree. Certain mutations did abrogate T cell reactivity; however, natural variants comprising these mutations are reportedly rare and transient in nature, presumably due to fitness costs. Overall, despite a narrow bias, the TCR accommodated frequent mutations by acting like a blanket over the hypervariable epitope, thereby providing effective viral immunity. Our findings simultaneously advance the understanding of anti-HCV immunity and indicate the potential for cross-genotype HCV vaccines.


  • Organizational Affiliation
    • Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Parkville, Victoria 3000, Australia;

Macromolecule Content 

  • Total Structure Weight: 242.52 kDa 
  • Atom Count: 16,924 
  • Modeled Residue Count: 2,106 
  • Deposited Residue Count: 2,123 
  • Unique protein chains: 5

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
HLA class I histocompatibility antigen, B-8 alpha chain
A, F
276Homo sapiensMutation(s): 0 
Gene Names: HLA-BHLAB
UniProt & NIH Common Fund Data Resources
Find proteins for P01889 (Homo sapiens)
Explore P01889 
Go to UniProtKB:  P01889
PHAROS:  P01889
GTEx:  ENSG00000234745 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01889
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Beta-2-microglobulin
B, G
100Homo sapiensMutation(s): 0 
Gene Names: B2MCDABP0092HDCMA22P
UniProt & NIH Common Fund Data Resources
Find proteins for P61769 (Homo sapiens)
Explore P61769 
Go to UniProtKB:  P61769
PHAROS:  P61769
GTEx:  ENSG00000166710 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP61769
Sequence Annotations
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Reference Sequence
Find similar proteins by:  Sequence   |   3D Structure  
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
NS3-4A protein
C, H
9Orthohepacivirus hominisMutation(s): 0 
UniProt
Find proteins for X2G898 (Hepacivirus hominis)
Explore X2G898 
Go to UniProtKB:  X2G898
Entity Groups
UniProt GroupX2G898
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
DD31 TCR alpha chain
D, J, K
206Homo sapiensMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
DD31 TCR beta chain
E, I, L
245Homo sapiensMutation(s): 0 

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
IOD

Query on IOD



Download:Ideal Coordinates CCD File
AA [auth L]
M [auth D]
N [auth E]
O [auth E]
Q [auth G]
AA [auth L],
M [auth D],
N [auth E],
O [auth E],
Q [auth G],
S [auth I],
T [auth I],
U [auth J],
V [auth K],
W [auth K],
X [auth L],
Y [auth L]
IODIDE ION
I
XMBWDFGMSWQBCA-UHFFFAOYSA-M
NA

Query on NA



Download:Ideal Coordinates CCD File
P [auth E],
R [auth G],
Z [auth L]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free:  0.248 (Depositor), 0.268 (DCC) 
  • R-Value Work:  0.206 (Depositor), 0.229 (DCC) 
  • R-Value Observed: 0.209 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 74.16α = 90
b = 252.19β = 101.97
c = 79.45γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
PHASERphasing
BUSTER-TNTrefinement
PDB_EXTRACTdata extraction
Blu-Icedata collection
XDSdata reduction
BUSTERrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-11-12
    Type: Initial release
  • Version 1.1: 2014-12-24
    Changes: Database references
  • Version 1.2: 2017-10-11
    Changes: Data collection
  • Version 1.3: 2020-09-16
    Changes: Database references, Derived calculations, Structure summary
  • Version 1.4: 2023-09-20
    Changes: Data collection, Database references, Refinement description
  • Version 1.5: 2024-03-13
    Changes: Source and taxonomy
  • Version 1.6: 2024-11-06
    Changes: Structure summary