4O2E

A peptide complexed with HLA-B*3901


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.981 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.186 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

N alpha-terminal acetylation for T cell recognition: molecular basis of MHC class I-restricted n alpha-acetylpeptide presentation

Sun, M.Liu, J.Qi, J.Tefsen, B.Shi, Y.Yan, J.Gao, G.F.

(2014) J.Immunol. 192: 5509-5519

  • DOI: 10.4049/jimmunol.1400199
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • As one of the most common posttranslational modifications (PTMs) of eukaryotic proteins, N(α)-terminal acetylation (Nt-acetylation) generates a class of N(α)-acetylpeptides that are known to be presented by MHC class I at the cell surface. Although s ...

    As one of the most common posttranslational modifications (PTMs) of eukaryotic proteins, N(α)-terminal acetylation (Nt-acetylation) generates a class of N(α)-acetylpeptides that are known to be presented by MHC class I at the cell surface. Although such PTM plays a pivotal role in adjusting proteolysis, the molecular basis for the presentation and T cell recognition of N(α)-acetylpeptides remains largely unknown. In this study, we determined a high-resolution crystallographic structure of HLA (HLA)-B*3901 complexed with an N(α)-acetylpeptide derived from natural cellular processing, also in comparison with the unmodified-peptide complex. Unlike the α-amino-free P1 residues of unmodified peptide, of which the α-amino group inserts into pocket A of the Ag-binding groove, the N(α)-linked acetyl of the acetylated P1-Ser protrudes out of the groove for T cell recognition. Moreover, the Nt-acetylation not only alters the conformation of the peptide but also switches the residues in the α1-helix of HLA-B*3901, which may impact the T cell engagement. The thermostability measurements of complexes between N(α)-acetylpeptides and a series of MHC class I molecules derived from different species reveal reduced stability. Our findings provide the insight into the mode of N(α)-acetylpeptide-specific presentation by classical MHC class I molecules and shed light on the potential of acetylepitope-based immune intervene and vaccine development.


    Organizational Affiliation

    School of Life Sciences, University of Science and Technology of China, Hefei 230027, China; CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China;,CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; Research Network of Immunity and Health, Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China.,National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China; and.,CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China;,School of Life Sciences, University of Science and Technology of China, Hefei 230027, China; CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China; and Research Network of Immunity and Health, Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China gaof@im.ac.cn.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HLA class I histocompatibility antigen, B-39 alpha chain
A, D
274Homo sapiensMutation(s): 0 
Gene Names: HLA-B (HLAB)
Find proteins for P30475 (Homo sapiens)
Go to Gene View: HLA-B
Go to UniProtKB:  P30475
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Beta-2-microglobulin
B, E
99Homo 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
Peptide from ATP-dependent RNA helicase DDX3X
C, F
9Homo sapiensMutation(s): 0 
Gene Names: DDX3X (DBX, DDX3)
EC: 3.6.4.13
Find proteins for O00571 (Homo sapiens)
Go to Gene View: DDX3X
Go to UniProtKB:  O00571
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.981 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.186 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 79.939α = 90.00
b = 103.967β = 90.00
c = 122.424γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
HKL-2000data scaling
PHENIXrefinement
HKL-2000data collection
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-07-23
    Type: Initial release