Crystal structure of intracellular B30.2 domain of BTN3A3 mutant in complex with HMBPP

Experimental Data Snapshot

  • Resolution: 1.60 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.242 
  • R-Value Observed: 0.245 

Starting Model: experimental
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This is version 1.3 of the entry. See complete history


A Structural Change in Butyrophilin upon Phosphoantigen Binding Underlies Phosphoantigen-Mediated V gamma 9V delta 2 T Cell Activation.

Yang, Y.Li, L.Yuan, L.Zhou, X.Duan, J.Xiao, H.Cai, N.Han, S.Ma, X.Liu, W.Chen, C.C.Wang, L.Li, X.Chen, J.Kang, N.Chen, J.Shen, Z.Malwal, S.R.Liu, W.Shi, Y.Oldfield, E.Guo, R.T.Zhang, Y.

(2019) Immunity 50: 1043

  • DOI: https://doi.org/10.1016/j.immuni.2019.02.016
  • Primary Citation of Related Structures:  
    5ZXK, 5ZZ3, 6ISM, 6ITA, 6J06, 6J0G, 6J0K, 6J0L

  • PubMed Abstract: 

    Human Vγ9Vδ2 T cells respond to microbial infections and malignancy by sensing diphosphate-containing metabolites called phosphoantigens, which bind to the intracellular domain of butyrophilin 3A1, triggering extracellular interactions with the Vγ9Vδ2 T cell receptor (TCR). Here, we examined the molecular basis of this "inside-out" triggering mechanism. Crystal structures of intracellular butyrophilin 3A proteins alone or in complex with the potent microbial phosphoantigen HMBPP or a synthetic analog revealed key features of phosphoantigens and butyrophilins required for γδ T cell activation. Analyses with chemical probes and molecular dynamic simulations demonstrated that dimerized intracellular proteins cooperate in sensing HMBPP to enhance the efficiency of γδ T cell activation. HMBPP binding to butyrophilin doubled the binding force between a γδ T cell and a target cell during "outside" signaling, as measured by single-cell force microscopy. Our findings provide insight into the "inside-out" triggering of Vγ9Vδ2 T cell activation by phosphoantigen-bound butyrophilin, facilitating immunotherapeutic drug design.

  • Organizational Affiliation

    School of Pharmaceutical Sciences, Beijing Advanced Innovation Center for Structural Biology, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing 100084, China.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Butyrophilin subfamily 3 member A3
A, B, C, D
221Homo sapiensMutation(s): 1 
Gene Names: BTN3A3BTF3
UniProt & NIH Common Fund Data Resources
Find proteins for O00478 (Homo sapiens)
Explore O00478 
Go to UniProtKB:  O00478
PHAROS:  O00478
GTEx:  ENSG00000111801 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO00478
Sequence Annotations
  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
H6P BindingDB:  6J0G Kd: min: 1540, max: 4270 (nM) from 2 assay(s)
IC50: min: 4560, max: 3.33e+5 (nM) from 8 assay(s)
EC50: min: 0.06, max: 60 (nM) from 6 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.60 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.242 
  • R-Value Observed: 0.245 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 39.109α = 85.78
b = 67.108β = 86.88
c = 75.436γ = 86.9
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-04-03
    Type: Initial release
  • Version 1.1: 2019-04-10
    Changes: Data collection, Database references
  • Version 1.2: 2019-05-01
    Changes: Data collection, Database references
  • Version 1.3: 2023-11-22
    Changes: Data collection, Database references, Refinement description