8HJT

Crystal Structure of Intracellular B30.2 Domain of VpBTN3 and VpBTN2 in Complex with HMBPP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.91 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.224 

Starting Model: experimental
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This is version 1.4 of the entry. See complete history


Literature

Phosphoantigens glue butyrophilin 3A1 and 2A1 to activate V gamma 9V delta 2 T cells.

Yuan, L.Ma, X.Yang, Y.Qu, Y.Li, X.Zhu, X.Ma, W.Duan, J.Xue, J.Yang, H.Huang, J.W.Yi, S.Zhang, M.Cai, N.Zhang, L.Ding, Q.Lai, K.Liu, C.Zhang, L.Liu, X.Yao, Y.Zhou, S.Li, X.Shen, P.Chang, Q.Malwal, S.R.He, Y.Li, W.Chen, C.Chen, C.C.Oldfield, E.Guo, R.T.Zhang, Y.

(2023) Nature 621: 840-848

  • DOI: https://doi.org/10.1038/s41586-023-06525-3
  • Primary Citation of Related Structures:  
    8HJT, 8IGT, 8IH4, 8IXV, 8IZE, 8IZG, 8JY9, 8JYA, 8JYB, 8JYC, 8JYE, 8JYF

  • PubMed Abstract: 

    In both cancer and infections, diseased cells are presented to human Vγ9Vδ2 T cells through an 'inside out' signalling process whereby structurally diverse phosphoantigen (pAg) molecules are sensed by the intracellular domain of butyrophilin BTN3A1 1-4 . Here we show how-in both humans and alpaca-multiple pAgs function as 'molecular glues' to promote heteromeric association between the intracellular domains of BTN3A1 and the structurally similar butyrophilin BTN2A1. X-ray crystallography studies visualized that engagement of BTN3A1 with pAgs forms a composite interface for direct binding to BTN2A1, with various pAg molecules each positioned at the centre of the interface and gluing the butyrophilins with distinct affinities. Our structural insights guided mutagenesis experiments that led to disruption of the intracellular BTN3A1-BTN2A1 association, abolishing pAg-mediated Vγ9Vδ2 T cell activation. Analyses using structure-based molecular-dynamics simulations, 19 F-NMR investigations, chimeric receptor engineering and direct measurement of intercellular binding force revealed how pAg-mediated BTN2A1 association drives BTN3A1 intracellular fluctuations outwards in a thermodynamically favourable manner, thereby enabling BTN3A1 to push off from the BTN2A1 ectodomain to initiate T cell receptor-mediated γδ T cell activation. Practically, we harnessed the molecular-glue model for immunotherapeutics design, demonstrating chemical principles for developing both small-molecule activators and inhibitors of human γδ T cell function.


  • Organizational Affiliation

    Tsinghua-Peking Center for Life Sciences, State Key Laboratory of Membrane Biology, School of Pharmaceutical Sciences, Tsinghua University, Beijing, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
butyrophilin subfamily 2 member A2
A, B
233Vicugna pacosMutation(s): 0 
Gene Names: LOC102538576
UniProt
Find proteins for A0A6J0B3M7 (Vicugna pacos)
Explore A0A6J0B3M7 
Go to UniProtKB:  A0A6J0B3M7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A6J0B3M7
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Butyrophylin 3
C, D
198Vicugna 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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.91 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.224 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.188α = 90
b = 78.188β = 90
c = 299.827γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
SAINTdata reduction
SAINTdata scaling
PHASERphasing
PDB_EXTRACTdata extraction

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: 2023-09-13
    Type: Initial release
  • Version 1.1: 2023-09-20
    Changes: Database references
  • Version 1.2: 2023-10-11
    Changes: Database references
  • Version 1.3: 2023-10-18
    Changes: Database references
  • Version 1.4: 2024-11-27
    Changes: Refinement description, Structure summary