4O2C

An Nt-acetylated peptide complexed with HLA-B*3901

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.802 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.174 

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;




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HLA class I histocompatibility antigen, B-39 alpha chain
A
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
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
10Homo 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
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
ACE
Query on ACE
C
NON-POLYMERC2 H4 O

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.802 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.174 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 50.845α = 90.00
b = 81.459β = 90.00
c = 110.958γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
HKL-2000data collection
HKL-2000data reduction
PHASERphasing
PHENIXrefinement

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

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