6J06

Crystal structure of intracellular B30.2 domain of BTN3A1 in complex with HMBPP-08

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.174 

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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) ...

    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
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Butyrophilin subfamily 3 member A1
A, B, C
196Homo sapiensMutation(s): 0 
Gene Names: BTN3A1, BTF5
UniProt & NIH Common Fund Data Resources
Find proteins for O00481 (Homo sapiens)
Explore O00481 
Go to UniProtKB:  O00481
PHAROS:  O00481
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO00481
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
99C
Query on 99C
Download Ideal Coordinates CCD File 
D [auth A],
K [auth B],
R [auth C]		(2E)-3-(hydroxymethyl)-4-(4-methylphenyl)but-2-en-1-yl trihydrogen diphosphate
C12 H18 O8 P2
UZMNPEQMXYMHTH-WUXMJOGZSA-N		 Ligand Interaction
FLC
Query on FLC
Download Ideal Coordinates CCD File 
J [auth A]CITRATE ANION
C6 H5 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-K		 Ligand Interaction
SO4
Query on SO4
Download Ideal Coordinates CCD File 
E [auth A]
F [auth A]
G [auth A]
H [auth A]
I [auth A]
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
L [auth B],
M [auth B],
N [auth B],
O [auth B],
P [auth B],
S [auth C],
T [auth C],
U [auth C]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L		 Ligand Interaction
CA
Query on CA
Download Ideal Coordinates CCD File 
Q [auth B]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.174 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 112.929α = 90
b = 211.588β = 90
c = 56.269γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


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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