5WSH

Structure of HLA-A2 P130

DOI: 10.2210/pdb5WSH/pdb

Classification: IMMUNE SYSTEM
Organism(s): Homo sapiens
Expression System: Escherichia coli K-12
Mutation(s): Yes

Deposited: 2016-12-07 Released: 2017-12-20
Deposition Author(s): Zhang, Y., Wu, Y., Qi, J., Liu, J., Gao, G.F., Meng, S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.196
R-Value Work: 0.162
R-Value Observed: 0.163

wwPDB Validation 3D Report Full Report

This is version 1.1 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

PubMed: 29950410 Search on PubMedSearch on PubMed Central
DOI: 10.1128/JVI.02120-17
Primary Citation of 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:

University of Chinese Academy of Sciences, Beijing, China.

Macromolecules

Find similar proteins by:

(by identity cutoff) | Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HLA class I histocompatibility antigen, A-2 alpha chain	A	275	Homo sapiens	Mutation(s): 1 Gene Names: HLA-A, HLAA
Find proteins for P04439 (Homo sapiens) Explore P04439 Go to UniProtKB: P04439
NIH Common Fund Data Resources
PHAROS P04439 GTEx ENSG00000206503
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Reference Sequence

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(by identity cutoff) | Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-2-microglobulin	B	100	Homo sapiens	Mutation(s): 0 Gene Names: B2M, CDABP0092, HDCMA22P
Find proteins for P61769 (Homo sapiens) Explore P61769 Go to UniProtKB: P61769
NIH Common Fund Data Resources
PHAROS P61769 GTEx ENSG00000166710
Protein Feature View Expand
Reference Sequence

Find similar proteins by: Sequence | Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
GLY-VAL-TRP-ILE-ARG-THR-PRO-THR-ALA	C	9	Homo sapiens	Mutation(s): 0
Protein Feature View Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PEG Query on PEG Download CCD File	A, B	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Ligand Interaction