9LN2 | pdb_00009ln2

Crystal Structure of Intracellular B30.2 Domain of VpBTN3 in Complex with DMASPP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.77 Å
  • R-Value Free: 
    0.202 (Depositor), 0.209 (DCC) 
  • R-Value Work: 
    0.157 (Depositor), 0.171 (DCC) 
  • R-Value Observed: 
    0.159 (Depositor) 

Starting Model: experimental
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Literature

Molecular glue binding behavior of phosphoantigens to alpaca butyrophilins.

Liu, C.Yi, S.Zhang, M.Chen, C.C.Liu, Y.Zhang, Z.Guo, R.T.Yang, Y.

(2025) J Biological Chem 301: 108555-108555

  • DOI: https://doi.org/10.1016/j.jbc.2025.108555
  • Primary Citation of Related Structures:  
    9LN2, 9LNZ

  • PubMed Abstract: 

    Vγ9Vδ2 T cells that respond to phosphoantigen (pAg) function as crucial sentinels of the immune system to eradicate pathogen-infected cells and tumor cells. Alpaca (Vicugna pacos) is the first nonprimate species identified to possess the pAg-reactive Vγ9Vδ2 T cell subset. However, the molecular mechanism accounting for the pAg recognition of alpaca Vγ9Vδ2 T cells remains unclear. Here, we report the crystal structures of alpaca butyrophilin 3 (VpBTN3) B30.2 domain in complex with the exogenous pAg analog, HMBPP-08, which is a valuable tool for studying the mechanism of butyrophilin-dependent Vγ9Vδ2 T cell activation, and the endogenous pAg analogue, dimethylallyl (S)-thiolodiphosphate (DMASPP). We elucidated that the function of pAgs is governed by their structural differences. Notably, DMASPP acts as a molecular glue in the interaction between the intracellular B30.2 domains of heterologous butyrophilins in alpaca and human. Interestingly, although HMBPP-08 has stronger affinity than DMASPP to VpBTN3 B30.2 domain, HMBPP-08 did not promote heterologous VpBTNs interaction. These findings establish a novel theoretical framework elucidating the mechanisms of Vγ9Vδ2 T cell activation and demonstrate the conserved evolutionary mechanisms underlying cross-species immune adaptation.


  • Organizational Affiliation
    • State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Hongshan Laboratory, School of Life Sciences, Hubei University, Wuhan, PR China.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Butyrophylin 3
A, B
242Vicugna pacosMutation(s): 0 
Gene Names: Btn3
UniProt
Find proteins for A0A345DF50 (Vicugna pacos)
Explore A0A345DF50 
Go to UniProtKB:  A0A345DF50
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A345DF50
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DST (Subject of Investigation/LOI)
Query on DST

Download Ideal Coordinates CCD File 
G [auth B]DIMETHYLALLYL S-THIOLODIPHOSPHATE
C5 H12 O6 P2 S
ZWFWSISPSBLNGO-UHFFFAOYSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
E [auth A],
F [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
EDO
Query on EDO

Download Ideal Coordinates CCD File 
H [auth B]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.77 Å
  • R-Value Free:  0.202 (Depositor), 0.209 (DCC) 
  • R-Value Work:  0.157 (Depositor), 0.171 (DCC) 
  • R-Value Observed: 0.159 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 43.858α = 90
b = 67.988β = 90
c = 134.307γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
SAINTdata reduction
SAINTdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China82271887

Revision History  (Full details and data files)

  • Version 1.0: 2025-05-14
    Type: Initial release
  • Version 1.1: 2025-09-03
    Changes: Database references