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 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.209 

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Ligand Structure Quality Assessment 


This is version 1.2 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: 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) ...

    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. Electronic address: zhangyonghui@tsinghua.edu.cn.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Butyrophilin subfamily 3 member A1A196Homo 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
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / 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
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
H6P Binding MOAD:  5ZXK Kd: 3300 (nM) from 1 assay(s)
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: 60 (nM) from 6 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.96 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.209 
  • 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

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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