6ILG

CRYSTAL STRUCTURE OF BAT MHC CLASS I PTAL-N*01:01 FOR 2.6 ANGSTROM


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.213 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Structure and Peptidome of the Bat MHC Class I Molecule Reveal a Novel Mechanism Leading to High-Affinity Peptide Binding.

Qu, Z.Li, Z.Ma, L.Wei, X.Zhang, L.Liang, R.Meng, G.Zhang, N.Xia, C.

(2019) J Immunol. 202: 3493-3506

  • DOI: 10.4049/jimmunol.1900001
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Bats are natural reservoir hosts, harboring more than 100 viruses, some of which are lethal to humans. The asymptomatic coexistence with viruses is thought to be connected to the unique immune system of bats. MHC class I (MHC I) presentation is close ...

    Bats are natural reservoir hosts, harboring more than 100 viruses, some of which are lethal to humans. The asymptomatic coexistence with viruses is thought to be connected to the unique immune system of bats. MHC class I (MHC I) presentation is closely related to cytotoxic lymphocyte immunity, which plays an important role in viral resistance. To investigate the characteristics of MHC I presentation in bats, the crystal structures of peptide-MHC I complexes of Pteropus alecto , Ptal-N*01:01/HEV-1 (DFANTFLP) and Ptal-N*01:01/HEV-2 (DYINTNLVP), and two related mutants, Ptal-N*01:01/HEV-1 PΩL (DFANTFLL) and Ptal-N*01:01 ΔMDL /HEV-1, were determined. Through structural analysis, we found that Ptal-N*01:01 had a multi-Ala-assembled pocket B and a flexible hydrophobic pocket F, which could accommodate variable anchor residues and allow Ptal-N*01:01 to bind numerous peptides. Three sequential amino acids, Met, Asp, and Leu, absent from the α1 domain of the H chain in other mammals, were present in this domain in the bat. Upon deleting these amino acids and determining the structure in p/Ptal-N*01:01 ΔMDL /HEV-1, we found they helped form an extra salt-bridge chain between the H chain and the N-terminal aspartic acid of the peptide. By introducing an MHC I random peptide library for de novo liquid chromatography-tandem mass spectrometry analysis, we found that this insertion module, present in all types of bats, can promote MHC I presentation of peptides with high affinity during the peptide exchange process. This study will help us better understand how bat MHC I presents high-affinity peptides from an extensive binding peptidome and provides a foundation to understand the cellular immunity of bats.


    Organizational Affiliation

    Key Laboratory of Animal Epidemiology, Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Haidian District, Beijing 100094, China.,Department of Microbiology and Immunology, College of Veterinary Medicine, China Agricultural University, Haidian District, Beijing 100094, China.,Department of Veterinary Biomedicine, College of Veterinary Medicine, China Agricultural University, Haidian District, Beijing 100094, China; and.,Department of Microbiology and Immunology, College of Veterinary Medicine, China Agricultural University, Haidian District, Beijing 100094, China; zhangnianzhi@cau.edu.cn xiachun@cau.edu.cn.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
MHC class I antigen
A
279Pteropus alectoMutation(s): 0 
Gene Names: Ptal-N
Find proteins for A0A125R585 (Pteropus alecto)
Go to UniProtKB:  A0A125R585
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Beta-2-microglobulin
B
98Pteropus alectoMutation(s): 0 
Find proteins for L5K3Y9 (Pteropus alecto)
Go to UniProtKB:  L5K3Y9
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
HEV-1-P8L
C
8Hendra virus (isolate Horse/Autralia/Hendra/1994)Mutation(s): 0 
Gene Names: P/V/C
Find proteins for O55778 (Hendra virus (isolate Horse/Autralia/Hendra/1994))
Go to UniProtKB:  O55778
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.213 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 72.876α = 90.00
b = 86.440β = 90.00
c = 135.121γ = 90.00
Software Package:
Software NamePurpose
HKL-3000data reduction
PHENIXrefinement
HKL-3000data scaling
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2019-07-24
    Type: Initial release