Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 22.92 kDa 
• Atom Count: 1664 
• Modelled Residue Count: 186 
• Deposited Residue Count: 196 
• Unique protein chains: 1

5ZXK

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

• PDB DOI: 10.2210/pdb5ZXK/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2018-05-21 Released: 2019-04-03 
• Deposition Author(s): Yang, Y.Y., Liu, W.D., Chen, C.C., Guo, R.T., Zhang, Y.H.

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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 

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

• PubMed: 30902636 
• 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). 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.

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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: [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Butyrophilin subfamily 3 member A1	A	196	Homo sapiens	Mutation(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 GTEx:  ENSG00000026950

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
H6P (Subject of Investigation/LOI)	B [auth A]	(2E)-4-hydroxy-3-methylbut-2-en-1-yl trihydrogen diphosphate C5 H12 O8 P2 MDSIZRKJVDMQOQ-GORDUTHDSA-N

Binding Affinity Annotations
ID	Source	Binding 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 = 45.131	α = 90
b = 125.668	β = 90
c = 39.046	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2018-05-21 
• Released Date: 2019-04-03 
Deposition Author(s): Yang, Y.Y., Liu, W.D., Chen, C.C., Guo, R.T., Zhang, Y.H.

Revision History  

• 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