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- PDB-5zz3: Crystal structure of intracellular B30.2 domain of BTN3A3 -

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Basic information

Entry
Database: PDB / ID: 5zz3
TitleCrystal structure of intracellular B30.2 domain of BTN3A3
ComponentsButyrophilin, subfamily 3, member A3 isoform b variant
KeywordsSIGNALING PROTEIN / Butyrophilin
Function / homology
Function and homology information


Butyrophilin (BTN) family interactions / T cell mediated immunity / regulation of cytokine production / ubiquitin protein ligase activity / T cell receptor signaling pathway / regulation of gene expression / protein ubiquitination / nuclear body / signaling receptor binding / innate immune response ...Butyrophilin (BTN) family interactions / T cell mediated immunity / regulation of cytokine production / ubiquitin protein ligase activity / T cell receptor signaling pathway / regulation of gene expression / protein ubiquitination / nuclear body / signaling receptor binding / innate immune response / external side of plasma membrane / intracellular membrane-bounded organelle / nucleoplasm / membrane / plasma membrane / cytoplasm / 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 ...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 / Butyrophilin, subfamily 3, member A3 isoform b variant
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsYang, Y.Y. / Li, X. / Liu, W.D. / 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
DepositionMay 30, 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 isoform b variant


Theoretical massNumber of molelcules
Total (without water)32,5631
Polymers32,5631
Non-polymers00
Water1448
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: light scattering, Monomer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area9330 Å2
Unit cell
Length a, b, c (Å)50.308, 50.308, 261.093
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Butyrophilin, subfamily 3, member A3 isoform b variant


Mass: 32563.338 Da / Num. of mol.: 1 / Fragment: UNP residues 24-280
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PET28A / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q59F79, UniProt: O00478*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: H2O

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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: 2.54 Å3/Da / Density % sol: 51.51 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: SODIUM CITRATE, IMIDAZOLE PH 8.0, 1 -PROPANOL., VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9793 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jan 8, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 7487 / % possible obs: 100 % / Redundancy: 23.6 % / CC1/2: 0.994 / Net I/σ(I): 46.625
Reflection shellResolution: 3→3.05 Å / Rmerge(I) obs: 0.654 / Num. unique obs: 334 / % possible all: 100

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Processing

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

4n7u


Resolution: 3→50 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.887 / SU B: 16.118 / SU ML: 0.286 / Cross valid method: THROUGHOUT / ESU R: 0.828 / ESU R Free: 0.394 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.275 374 5 %RANDOM
Rwork0.195 ---
obs0.199 7044 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 98.74 Å2
Baniso -1Baniso -2Baniso -3
1-6.54 Å20 Å20 Å2
2--6.54 Å20 Å2
3----13.09 Å2
Refinement stepCycle: LAST / Resolution: 3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1552 0 0 8 1560
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0191601
X-RAY DIFFRACTIONr_bond_other_d0.0020.021468
X-RAY DIFFRACTIONr_angle_refined_deg1.9091.9512181
X-RAY DIFFRACTIONr_angle_other_deg1.04333393
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.1985190
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.67423.33378
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.22415255
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.4851512
X-RAY DIFFRACTIONr_chiral_restr0.0960.2227
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211792
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02374
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_it8.3979.65763
X-RAY DIFFRACTIONr_mcbond_other8.3889.646762
X-RAY DIFFRACTIONr_mcangle_it11.63414.48952
X-RAY DIFFRACTIONr_mcangle_other11.6314.485953
X-RAY DIFFRACTIONr_scbond_it8.11410.128838
X-RAY DIFFRACTIONr_scbond_other8.1110.132839
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other11.60314.9711230
X-RAY DIFFRACTIONr_long_range_B_refined14.4677.071798
X-RAY DIFFRACTIONr_long_range_B_other14.45677.1011799
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3→3.08 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.319 22 -
Rwork0.206 494 -
obs--99.81 %

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