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- PDB-8jyc: Crystal Structure of Intracellular B30.2 Domain of BTN3A1 and BTN... -

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Basic information

Entry
Database: PDB / ID: 8jyc
TitleCrystal Structure of Intracellular B30.2 Domain of BTN3A1 and BTN2A1 in Complex with DMAPP
Components(Butyrophilin subfamily ...) x 2
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 / lipid metabolic process / positive regulation of type II interferon production / T cell receptor signaling pathway / adaptive immune response / external side of plasma membrane / signaling receptor binding / plasma membrane
Similarity search - Function
Butyrophilin subfamily 1/2, SPRY/PRY 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 ...Butyrophilin subfamily 1/2, SPRY/PRY 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
DIMETHYLALLYL DIPHOSPHATE / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Butyrophilin subfamily 3 member A1 / Butyrophilin subfamily 2 member A1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.29 Å
AuthorsYuan, L.J. / Yang, Y.Y. / Li, X. / Cai, N.N. / Chen, C.-C. / Guo, R.-T. / Zhang, Y.H.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32100711 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
DepositionJul 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 2 member A1
B: Butyrophilin subfamily 2 member A1
C: Butyrophilin subfamily 3 member A1
D: Butyrophilin subfamily 3 member A1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,67025
Polymers94,6774
Non-polymers2,99321
Water5,945330
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12900 Å2
ΔGint32 kcal/mol
Surface area33320 Å2
Unit cell
Length a, b, c (Å)90.153, 90.153, 167.918
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number76
Space group name H-MP41

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Components

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Butyrophilin subfamily ... , 2 types, 4 molecules ABCD

#1: Protein Butyrophilin subfamily 2 member A1


Mass: 24676.881 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BTN2A1, BT2.1, BTF1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q7KYR7
#2: Protein Butyrophilin subfamily 3 member A1


Mass: 22661.773 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BTN3A1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O00481

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Non-polymers , 7 types, 351 molecules

#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#5: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#6: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#7: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: C4H10O3
#8: Chemical ChemComp-DMA / DIMETHYLALLYL DIPHOSPHATE


Mass: 246.092 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H12O7P2 / Feature type: SUBJECT OF INVESTIGATION
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 330 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.92 Å3/Da / Density % sol: 68.61 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / Details: 42% PEG200, 0.1 M HEPES pH7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 4, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.29→50 Å / Num. obs: 60267 / % possible obs: 100 % / Redundancy: 13.7 % / Rmerge(I) obs: 0.119 / Rpim(I) all: 0.033 / Rrim(I) all: 0.123 / Χ2: 0.75 / Net I/σ(I): 4 / Num. measured all: 825425
Reflection shell

Diffraction-ID: 1 / % possible all: 100

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2
2.29-2.3713.40.72960500.9140.2070.7580.721
2.37-2.4714.10.58959590.9440.1630.6110.695
2.47-2.5813.90.53960270.9470.150.560.8
2.58-2.7213.40.44360040.9690.1260.460.859
2.72-2.8913.20.27160140.9860.0770.2810.734
2.89-3.1114.20.19160240.9930.0520.1980.722
3.11-3.42140.13359970.9970.0370.1380.778
3.42-3.9213.40.10660500.9980.030.110.972
3.92-4.9314.20.05660280.9990.0150.0580.662
4.93-5013.40.04861140.9990.0140.050.568

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ZXK

5zxk


Resolution: 2.29→47.6 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.938 / SU B: 4.983 / SU ML: 0.121 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.186 / ESU R Free: 0.172 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2163 3012 5 %RANDOM
Rwork0.1709 ---
obs0.1731 57126 99.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 118.18 Å2 / Biso mean: 40.249 Å2 / Biso min: 20.95 Å2
Baniso -1Baniso -2Baniso -3
1-0.87 Å2-0 Å2-0 Å2
2--0.87 Å2-0 Å2
3----1.73 Å2
Refinement stepCycle: final / Resolution: 2.29→47.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6127 0 194 330 6651
Biso mean--59.34 47.31 -
Num. residues----761
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0136496
X-RAY DIFFRACTIONr_bond_other_d0.0010.0175999
X-RAY DIFFRACTIONr_angle_refined_deg1.7131.6638767
X-RAY DIFFRACTIONr_angle_other_deg1.261.59513919
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.2375761
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.45420.691362
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.264151024
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2591557
X-RAY DIFFRACTIONr_chiral_restr0.0750.2785
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.027090
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021437
LS refinement shellResolution: 2.29→2.348 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.271 230 -
Rwork0.225 4179 -
obs--99.32 %

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