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- PDB-8ixv: Crystal structure of intracellular B30.2 domain of BTN3A in compl... -

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Basic information

Entry
Database: PDB / ID: 8ixv
TitleCrystal structure of intracellular B30.2 domain of BTN3A in complex with 2Cl-HMBPP
ComponentsButyrophilin subfamily 3 member A1
KeywordsSIGNALING PROTEIN / Butyrophilin
Function / homology
Function and homology information


Butyrophilin (BTN) family interactions / activated T cell proliferation / regulation of cytokine production / positive regulation of cytokine production / positive regulation of type II interferon production / T cell receptor signaling pathway / adaptive immune response / signaling receptor binding / external side of plasma membrane / plasma membrane
Similarity search - Function
Butyrophilin subfamily 3, PRY/SPRY domain / : / : / Butyrophilin subfamily 3 member A2-like, Ig-C domain / SPRY domain / SPRY-associated domain / SPRY-associated / PRY / Butyrophylin-like, SPRY domain / SPRY domain ...Butyrophilin subfamily 3, PRY/SPRY domain / : / : / Butyrophilin subfamily 3 member A2-like, Ig-C domain / SPRY domain / SPRY-associated domain / SPRY-associated / PRY / Butyrophylin-like, SPRY domain / SPRY domain / B30.2/SPRY domain / B30.2/SPRY domain profile. / B30.2/SPRY domain superfamily / Domain in SPla and the RYanodine Receptor. / SPRY domain / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Concanavalin A-like lectin/glucanase domain superfamily / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Jelly Rolls / Immunoglobulin-like fold / Sandwich / Mainly Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Chem-RZO / Butyrophilin subfamily 3 member A1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.72 Å
AuthorsYang, Y.Y. / Yi, S.M. / Huang, J.W. / Chen, C.C. / Guo, R.T.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Nature / Year: 2023
Title: Phosphoantigens glue butyrophilin 3A1 and 2A1 to activate V gamma 9V delta 2 T cells.
Authors: Yuan, L. / Ma, X. / Yang, Y. / Qu, Y. / Li, X. / Zhu, X. / Ma, W. / Duan, J. / Xue, J. / Yang, H. / Huang, J.W. / Yi, S. / Zhang, M. / Cai, N. / Zhang, L. / Ding, Q. / Lai, K. / Liu, C. / ...Authors: Yuan, L. / Ma, X. / Yang, Y. / Qu, Y. / Li, X. / Zhu, X. / Ma, W. / Duan, J. / Xue, J. / Yang, H. / Huang, J.W. / Yi, S. / Zhang, M. / Cai, N. / Zhang, L. / Ding, Q. / Lai, K. / Liu, C. / Zhang, L. / Liu, X. / Yao, Y. / Zhou, S. / Li, X. / Shen, P. / Chang, Q. / Malwal, S.R. / He, Y. / Li, W. / Chen, C. / Chen, C.C. / Oldfield, E. / Guo, R.T. / Zhang, Y.
History
DepositionApr 3, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 13, 2023Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: Database references / Category: citation / citation_author / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Oct 11, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 18, 2023Group: Database references / Category: citation_author / Item: _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Butyrophilin subfamily 3 member A1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,1594
Polymers22,6621
Non-polymers4973
Water4,774265
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area210 Å2
ΔGint1 kcal/mol
Surface area9210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.774, 61.944, 75.405
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab

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Components

#1: Protein Butyrophilin subfamily 3 member A1


Mass: 22661.773 Da / Num. of mol.: 1 / Fragment: UNP residues 328-513
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BTN3A1 / Production host: Escherichia coli (E. coli) / References: UniProt: O00481
#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-RZO / [bis(chloranyl)-[[(E)-3-methyl-4-oxidanyl-but-2-enoxy]-oxidanyl-phosphoryl]methyl]phosphonic acid


Mass: 329.009 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H12Cl2O7P2 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 265 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.5 Å3/Da / Density % sol: 50.79 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / Details: Calcium acetate hydrate, PEG8000,Sodium citrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: LIQUID ANODE / Type: BRUKER METALJET / Wavelength: 1.34 Å
DetectorType: Bruker PHOTON III / Detector: PIXEL / Date: Mar 27, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.34 Å / Relative weight: 1
ReflectionResolution: 1.72→45.77 Å / Num. obs: 23485 / % possible obs: 98.9 % / Redundancy: 8.46 % / Biso Wilson estimate: 20.55 Å2 / Rmerge(I) obs: 0.0482 / Net I/σ(I): 24.96
Reflection shellResolution: 1.72→1.82 Å / Rmerge(I) obs: 0.2179 / Num. unique obs: 1167

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
SAINTdata reduction
SADABSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.72→32.21 Å / SU ML: 0.2105 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.2345
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2438 1144 4.94 %RANDOM
Rwork0.2001 21995 --
obs0.2022 23139 98.77 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.12 Å2
Refinement stepCycle: LAST / Resolution: 1.72→32.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1514 0 28 265 1807
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00721585
X-RAY DIFFRACTIONf_angle_d1.1012155
X-RAY DIFFRACTIONf_chiral_restr0.0693228
X-RAY DIFFRACTIONf_plane_restr0.0077274
X-RAY DIFFRACTIONf_dihedral_angle_d10.4179213
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.72-1.80.3441270.27262740X-RAY DIFFRACTION99.79
1.8-1.890.26941520.23272722X-RAY DIFFRACTION99.97
1.89-2.010.23241430.20742749X-RAY DIFFRACTION100
2.01-2.170.26461630.21082733X-RAY DIFFRACTION100
2.17-2.380.25871350.20392779X-RAY DIFFRACTION100
2.39-2.730.26051520.20872761X-RAY DIFFRACTION100
2.73-3.440.2151560.1852800X-RAY DIFFRACTION99.8
3.44-32.210.23021160.1862711X-RAY DIFFRACTION91.16

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