3OXS | pdb_00003oxs

Crystal Structure of HLA A*02:07 Bound to HBV Core 18-27


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 
    0.207 (Depositor), 0.207 (DCC) 
  • R-Value Work: 
    0.177 (Depositor), 0.175 (DCC) 
  • R-Value Observed: 
    0.179 (Depositor) 

Starting Model: experimental
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This is version 1.3 of the entry. See complete history

Literature

Structural insights into the binding of hepatitis B virus core peptide to HLA-A2 alleles: Towards designing better vaccines.

Liu, J.Chen, K.Y.Ren, E.C.

(2011) Eur J Immunol 41: 2097-2106

  • DOI: https://doi.org/10.1002/eji.201041370
  • Primary Citation Related Structures: 
    3OX8, 3OXR, 3OXS

  • PubMed Abstract: 

    Binding of specific antigenic peptides with human leukocyte antigen (HLA) molecules is a prerequisite for the initiation of T-cell responses and structural information about the peptide-HLA complex is essential for the detailed understanding of such interactions. HLA-A2 is the most prevalent HLA allele globally but aside from A*02:01 there is a significant lack of crystal structures, particularly for alleles that occur in high frequencies among Asian populations. Here, we report three HLA-A2 structures with the immunodominant hepatitis B core antigen 18-27 (HBcAg18-27) epitope, namely A*02:03, A*02:06, and A*02:07 at resolutions of 2.16, 1.70, and 1.75 Å respectively. This comparative analysis reveals that minor polymorphic residue changes between different HLA alleles can induce significant alterations in the major histocompatibility complex-peptide interface, and introduce conformational changes in the p3-p8 peptide region. Circular dichroism analysis demonstrated the HLA-A2-peptide complexes to have a hierarchy of thermostability and binding affinity in the order of A*02:06>A*02:07>A*02:01>A*02:03. Our findings provide structural insights into the varied HLA-A2 allele binding of the hepatitis B core antigen 18-27 epitope and the data suggest that chemical modifications of the peptide side chains could be a promising strategy to modulate and improve HLA-A2-peptide binding affinity for vaccine design.


  • Organizational Affiliation
    • Singapore Immunology Network, A*STAR, Immunos, Singapore.

Macromolecule Content 

  • Total Structure Weight: 44.83 kDa 
  • Atom Count: 3,584 
  • Modeled Residue Count: 385 
  • Deposited Residue Count: 385 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
MHC class I antigen275Homo sapiensMutation(s): 0 
Gene Names: HLA-AMHC HLA-A*02:07
UniProt
Find proteins for Q861F6 (Homo sapiens)
Explore Q861F6 
Go to UniProtKB:  Q861F6
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UniProt GroupQ861F6
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Beta-2-microglobulin100Homo sapiensMutation(s): 0 
Gene Names: B2MBETA 2-MICROGLOBULINCDABP0092HDCMA22P
UniProt & NIH Common Fund Data Resources
Find proteins for P61769 (Homo sapiens)
Explore P61769 
Go to UniProtKB:  P61769
PHAROS:  P61769
GTEx:  ENSG00000166710 
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UniProt GroupP61769
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
10mer peptide from Pre-core-protein10Hepatitis B virusMutation(s): 0 
UniProt
Find proteins for P0C6H2 (Hepatitis B virus genotype C (isolate Vietnam/3270/2000))
Explore P0C6H2 
Go to UniProtKB:  P0C6H2
Entity Groups
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UniProt GroupP0C6H2
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free:  0.207 (Depositor), 0.207 (DCC) 
  • R-Value Work:  0.177 (Depositor), 0.175 (DCC) 
  • R-Value Observed: 0.179 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.21α = 90
b = 79.06β = 90
c = 110γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
AMoREphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-05-04
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2023-11-01
    Changes: Data collection, Database references, Refinement description
  • Version 1.3: 2024-10-09
    Changes: Structure summary