5ZXK

Crystal structure of intracellular B30.2 domain of BTN3A1 in complex with HMBPP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.96 Å
  • R-Value Free: 
    0.265 (Depositor), 0.270 (DCC) 
  • R-Value Work: 
    0.206 (Depositor), 0.220 (DCC) 
  • R-Value Observed: 
    0.209 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted H6PClick on this verticalbar to view details

This is version 1.3 of the entry. See complete history


Literature

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.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Butyrophilin subfamily 3 member A1196Homo sapiensMutation(s): 0 
Gene Names: BTN3A1BTF5
UniProt & NIH Common Fund Data Resources
Find proteins for O00481 (Homo sapiens)
Explore O00481 
Go to UniProtKB:  O00481
PHAROS:  O00481
GTEx:  ENSG00000026950 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO00481
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
H6P (Subject of Investigation/LOI)
Query on H6P

Download Ideal Coordinates CCD File 
B [auth A](2E)-4-hydroxy-3-methylbut-2-en-1-yl trihydrogen diphosphate
C5 H12 O8 P2
MDSIZRKJVDMQOQ-GORDUTHDSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
H6P BindingDB:  5ZXK 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: 4.2 (nM) from 5 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.96 Å
  • R-Value Free:  0.265 (Depositor), 0.270 (DCC) 
  • R-Value Work:  0.206 (Depositor), 0.220 (DCC) 
  • R-Value Observed: 0.209 (Depositor) 
Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45.131α = 90
b = 125.668β = 90
c = 39.046γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
REFMACrefinement

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted H6PClick on this verticalbar to view details

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