5XOV

Crystal structure of peptide-HLA-A24 bound to S19-2 V-delta/V-beta TCR


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.684 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.203 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Conserved V delta 1 binding geometry in a setting of locus-disparate pHLA recognition by delta / alpha beta TCRs: insight into recognition of HIV peptides by TCR

Shi, Y.Kawana-Tachikawa, A.Gao, F.Qi, J.Liu, C.Gao, J.Cheng, H.Ueno, T.Iwamoto, A.Gao, G.F.

(2017) J. Virol. --: --

  • DOI: 10.1128/JVI.00725-17
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Given a limited set of TCR V genes which are used to create TCRs that are reactive to different ligands, such as MHC class I, MHC class II and MHC-like proteins (for example, MIC molecules and CD1 molecules), the Vδ1 segment can be rearranged with Dδ ...

    Given a limited set of TCR V genes which are used to create TCRs that are reactive to different ligands, such as MHC class I, MHC class II and MHC-like proteins (for example, MIC molecules and CD1 molecules), the Vδ1 segment can be rearranged with Dδ-Jδ-Cδ or Jα-Cα segments, to form classical γδTCR or uncommon αβTCR using a Vδ1 segment (δ/αβTCR). Here we have determined two complex structures of the δ/αβTCRs (S19-2 and TU55) bound to different locus-disparate MHCIs with HIV peptides (HLA-A*2402-Nef138-10 and HLA-B*3501-Pol448-9). The overall binding modes resemble classical αβTCRs, but display a strong tilt binding geometry of Vδ1 domain towards the HLA α1 helix, due to a conserved extensive interaction between the CDR1δ loop and N-terminal region of α1 helix (mainly in position 62). The aromatic amino acids of the CDR1δ loop exploit different conformations ("aromatic-ladder" or "aromatic-hairpin") to accommodate distinct MHC helical scaffolds. This tolerance helps to explain how a particular TCR V region can similarly dock onto multiple MHC molecules, and thus, may potentially explain the nature of TCR cross-reactivity. In addition, the length of CDR3δ loop could affect the extent of tilt binding of Vδ1 domain, and adaptively, the pairing Vβ domains adjust their mass centers to generate differential MHC contacts, hence probably ensuring the TCR specificity to a certain peptide-MHC. Our data have provided further structural insights into the TCR recognition of classical pMHCI molecules, unifying the cross-reactivity and specificity together.IMPORTANCE The specificity of αβ T cell recognition is determined by the CDR loops of the αβTCR and the general binding mode of αβTCRs to pMHC has been established over the last decade. Due to the intrinsic genomic structure of the TCR α/δ chain locus, some Vδ segments can rearrange with Cα segment, forming a hybrid VδCαVβCβ TCR, δ/αβTCR. However, the basis for the molecular recognition of such TCRs to their ligands is elusive. Here, an αβTCR using Vδ1 segment, S19-2, is isolated from a HIV-infected patient, in an HLA-A*24:02 restricted manner. Then we solved the crystal structures of S19-2 TCR and another δ/αβTCR TU55 binding to their ligands respectively, revealing a conserved Vδ1 binding feature. Further binding kinetics analysis reveals that the S19-2 and TU55 TCRs bind pHLA very tightly and long-lastingly. Our results illustrate the binding mode of a TCR using Vδ1 segment to its ligand, virus-derived pHLA.


    Organizational Affiliation

    CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HLA class I histocompatibility antigen, A-24 alpha chain
A, D
274Homo sapiensMutation(s): 0 
Gene Names: HLA-A (HLAA)
Find proteins for P05534 (Homo sapiens)
Go to Gene View: HLA-A
Go to UniProtKB:  P05534
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Beta-2-microglobulin
B, E
100Homo 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
HIV-1 Nef138-10 peptide
C, F
10Human immunodeficiency virus type 1 group M subtype BMutation(s): 0 
Gene Names: nef
Find proteins for P03407 (Human immunodeficiency virus type 1 group M subtype B)
Go to UniProtKB:  P03407
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
V-delta chain of T cell receptor
I, G
207N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
V-beta chain of T cell receptor
J, H
245N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.684 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.203 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 101.992α = 90.00
b = 73.789β = 90.00
c = 163.781γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
PHASERphasing
HKL-2000data scaling
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-06-14
    Type: Initial release
  • Version 1.1: 2017-09-27
    Type: Data collection
  • Version 1.2: 2017-11-22
    Type: Database references