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- PDB-6j0l: Crystal structure of intracellular B30.2 domain of BTN3A3 mutant ... -

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Basic information

Entry
Database: PDB / ID: 6j0l
TitleCrystal structure of intracellular B30.2 domain of BTN3A3 mutant in complex with sulfate ion
ComponentsButyrophilin subfamily 3 member A3
KeywordsSIGNALING PROTEIN / Butyrophilin
Function / homology
Function and homology information


Butyrophilin (BTN) family interactions / T cell mediated immunity / regulation of cytokine production / T cell receptor signaling pathway / nuclear body / signaling receptor binding / external side of plasma membrane / intracellular membrane-bounded organelle / nucleoplasm / membrane ...Butyrophilin (BTN) family interactions / T cell mediated immunity / regulation of cytokine production / T cell receptor signaling pathway / nuclear body / signaling receptor binding / external side of plasma membrane / intracellular membrane-bounded organelle / nucleoplasm / membrane / plasma membrane / cytosol
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
Butyrophilin subfamily 3 member A3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsYang, Y.Y. / Liu, W.D. / Cai, N.N. / Chen, C.C. / Guo, R.T. / Zhang, Y.H.
CitationJournal: Immunity / Year: 2019
Title: A Structural Change in Butyrophilin upon Phosphoantigen Binding Underlies Phosphoantigen-Mediated V gamma 9V delta 2 T Cell Activation.
Authors: 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. ...Authors: 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.
History
DepositionDec 24, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 3, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 10, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_id_ISSN / _citation.journal_volume ..._citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2May 1, 2019Group: Data collection / Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.3Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Butyrophilin subfamily 3 member A3
B: Butyrophilin subfamily 3 member A3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,31310
Polymers50,5452
Non-polymers7698
Water3,999222
1
A: Butyrophilin subfamily 3 member A3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,6575
Polymers25,2721
Non-polymers3844
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Butyrophilin subfamily 3 member A3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,6575
Polymers25,2721
Non-polymers3844
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Butyrophilin subfamily 3 member A3
B: Butyrophilin subfamily 3 member A3
hetero molecules

A: Butyrophilin subfamily 3 member A3
B: Butyrophilin subfamily 3 member A3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,62720
Polymers101,0904
Non-polymers1,53716
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_557-x,y,-z+21
Buried area9030 Å2
ΔGint-237 kcal/mol
Surface area31690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.067, 73.470, 74.896
Angle α, β, γ (deg.)90.00, 111.39, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Butyrophilin subfamily 3 member A3


Mass: 25272.418 Da / Num. of mol.: 2 / Fragment: UNP residues 328-515 / Mutation: R351H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BTN3A3, BTF3 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O00478
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 222 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsThe intracellular B30.2 domain of BTN3A3 was redesigned to have TEV protease cleavage sites and ...The intracellular B30.2 domain of BTN3A3 was redesigned to have TEV protease cleavage sites and bordering the linker region(AGAGA).

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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: 2.03 Å3/Da / Density % sol: 39.38 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: BIS-TRIS ,Ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 1 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Oct 2, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.95→25 Å / Num. obs: 28751 / % possible obs: 97.5 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.058 / Net I/σ(I): 31.37
Reflection shellResolution: 1.95→2.02 Å / Num. unique obs: 2900 / CC1/2: 0.88

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4N7U

4n7u


Resolution: 1.95→25 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.943 / SU B: 3.813 / SU ML: 0.109 / Cross valid method: THROUGHOUT / ESU R: 0.172 / ESU R Free: 0.164 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23435 1443 5 %RANDOM
Rwork0.176 ---
obs0.17882 27305 97.37 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 34.728 Å2
Baniso -1Baniso -2Baniso -3
1-1.99 Å20 Å2-2.92 Å2
2--1.35 Å2-0 Å2
3----0.81 Å2
Refinement stepCycle: 1 / Resolution: 1.95→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3062 0 40 222 3324
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0193193
X-RAY DIFFRACTIONr_bond_other_d0.0010.022888
X-RAY DIFFRACTIONr_angle_refined_deg1.3271.964355
X-RAY DIFFRACTIONr_angle_other_deg0.67236679
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.1515372
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.61923.462156
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.05215506
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2861522
X-RAY DIFFRACTIONr_chiral_restr0.0890.2456
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.0213529
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02741
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.6283.1071494
X-RAY DIFFRACTIONr_mcbond_other3.6293.1051493
X-RAY DIFFRACTIONr_mcangle_it4.6694.6421864
X-RAY DIFFRACTIONr_mcangle_other4.6684.6451865
X-RAY DIFFRACTIONr_scbond_it5.313.7061699
X-RAY DIFFRACTIONr_scbond_other5.1263.6741668
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.1125.3162444
X-RAY DIFFRACTIONr_long_range_B_refined8.85126.9483650
X-RAY DIFFRACTIONr_long_range_B_other8.84126.7223556
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.951→2.001 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.278 105 -
Rwork0.224 2038 -
obs--98.39 %

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