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 5E00 | pdb_00005e00

Structure of HLA-A2 P130


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 
    0.205 (Depositor), 0.206 (DCC) 
  • R-Value Work: 
    0.176 (Depositor), 0.178 (DCC) 
  • R-Value Observed: 
    0.177 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 5E00

This is version 1.2 of the entry. See complete history. 

Literature

CD8+T-Cell Response-Associated Evolution of Hepatitis B Virus Core Protein and Disease Progress.

Zhang, Y., Wu, Y., Deng, M., Xu, D., Li, X., Xu, Z., Hu, J., Zhang, H., Liu, K., Zhao, Y., Gao, F., Bi, S., Gao, G.F., Zhao, J., Liu, W.J., Meng, S.

(2018) J Virol 92

  • DOI: https://doi.org/10.1128/JVI.02120-17
  • Primary Citation Related Structures: 
    5E00, 5WSH

  • PubMed Abstract: 

    Under the immune pressure of cytotoxic T cells (CTLs), hepatitis B virus (HBV) evolves to accumulate mutations more likely within epitopes to evade immune detection. However, little is known about the specific patterns of the immune pressure-associated HBV mutation of T-cell epitopes and their link to disease progression. Here, we observed a correlation of the accumulated variants on HBV core protein (HBc) with the disease severity of HBV infection. Further analysis indicated that these substitutions were mostly located within CD8 + T-cell epitopes of HBc protein, which were systematically screened and identified in an unbiased manner in our study. From individual peptide level to the human leukocyte antigen I (HLA-I)-restricted population level, we elucidated that the mutations in these well-defined HLA-I-restricted T-cell epitopes significantly decreased antiviral activity-specific CTLs and were positively associated with clinical parameters and disease progression in HBV-infected patients. The molecular pattern for viral epitope variations based on the sequencing of 105 HBV virus genomes indicated that the C-terminal portion (Pc), especially the Pc-1 and Pc-2 positions, have the highest mutation rates. Further structural analysis of HLA-A*02 complexed to diverse CD8 + T-cell epitopes revealed that the highly variable C-terminal bulged peak of M-shaped HBc-derived epitopes are solvent exposed, and most of the CDR3βs of the T-cell receptor hover over them. These data shed light on the molecular and immunological mechanisms of T-cell immunity-associated viral evolution in hepatitis B progression, which is beneficial for designing immunotherapies and vaccines. IMPORTANCE The specific patterns of sequence polymorphisms of T-cell epitopes and the immune mechanisms of the HBV epitope mutation-linked disease progression are largely unclear. In this study, we systematically evaluated the contribution of CD8 + T cells to the disease progress-associated evolution of HBV. By evaluation of patient T-cell responses based on the peptide repertoire, we comprehensively characterized the association of clinical parameters in chronic hepatitis B with the antiviral T-cell response-associated mutations of the viruses from the single-epitope level to the overall HLA-I-restricted peptide levels. Furthermore, we investigated the molecular basis of the HLA-A2-restricted peptide immune escape and found that the solvent-exposed C-terminal portion of the epitopes is highly variable under CDR3β recognition. Our work may provide a comprehensive evaluation of viral mutations impacted by the host CTL response in HBV disease progression in the context of the full repertoire of HBc-derived epitopes.


  • Organizational Affiliation: 
    • CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, China.

Macromolecule Content 

  • Total Structure Weight: 44.83 kDa 
  • Atom Count: 3,667 
  • Modeled Residue Count: 384 
  • Deposited Residue Count: 384 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
HLA class I histocompatibility antigen, A-2 alpha chain275Homo sapiensMutation(s): 0 
Gene Names: HLA-A, HLAA
UniProt & NIH Common Fund Data Resources
Find proteins for P04439 (Homo sapiens)
Explore P04439 
Go to UniProtKB:  P04439
PHAROS:  P04439
GTEx:  ENSG00000206503 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP04439
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Beta-2-microglobulin100Homo sapiensMutation(s): 0 
Gene Names: B2M, CDABP0092, HDCMA22P
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
GLY-VAL-TRP-ILE-ARG-THR-PRO-PRO-ALA9Homo sapiensMutation(s): 0 
UniProt
Find proteins for Q76R61 (Hepatitis B virus genotype C subtype ayr (isolate Human/Japan/Okamoto/-))
Explore Q76R61 
Go to UniProtKB:  Q76R61
Entity Groups
UniProt GroupQ76R61
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SO4

Query on SO4



Download:Ideal Coordinates CCD File
D [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free:  0.205 (Depositor), 0.206 (DCC) 
  • R-Value Work:  0.176 (Depositor), 0.178 (DCC) 
  • R-Value Observed: 0.177 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.608α = 90
b = 72.006β = 90
c = 123.788γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
CNSdata reduction
CNSdata scaling
CNSphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-01-18
    Type: Initial release
  • Version 1.1: 2019-01-23
    Changes: Data collection, Database references
  • Version 1.2: 2024-11-20
    Changes: Advisory, Data collection, Database references, Structure summary