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- PDB-6ita: Crystal structure of intracellular B30.2 domain of BTN3A1 mutant -

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Basic information

Entry
Database: PDB / ID: 6ita
TitleCrystal structure of intracellular B30.2 domain of BTN3A1 mutant
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 / SPRY domain / : / : / Butyrophilin subfamily 3 member A2-like, Ig-C domain / SPRY-associated domain / SPRY-associated / PRY / Butyrophylin-like, SPRY domain / SPRY domain ...Butyrophilin subfamily 3, PRY/SPRY domain / SPRY domain / : / : / Butyrophilin subfamily 3 member A2-like, Ig-C 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 / Jelly Rolls / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Sandwich / Mainly Beta
Similarity search - Domain/homology
Butyrophilin subfamily 3 member A1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 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
DepositionNov 20, 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

Downloads & links

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Assembly

Deposited unit
A: Butyrophilin subfamily 3 member A1


Theoretical massNumber of molelcules
Total (without water)22,4321
Polymers22,4321
Non-polymers00
Water5,549308
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area9220 Å2
Unit cell
Length a, b, c (Å)46.961, 46.961, 158.996
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Butyrophilin subfamily 3 member A1


Mass: 22431.508 Da / Num. of mol.: 1 / Fragment: UNP residues 328-513 / Mutation: W350A, W391A
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 308 / 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: 1.95 Å3/Da / Density % sol: 37.05 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: Sodium Fluoride, Polyethylene Glycol 3350

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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: Nov 9, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.2→45.04 Å / Num. obs: 52887 / % possible obs: 98.62 % / Redundancy: 8.9 % / Rmerge(I) obs: 0.039 / Net I/σ(I): 57.27
Reflection shellResolution: 1.2→1.24 Å / Rmerge(I) obs: 0.452 / Num. unique obs: 5020 / CC1/2: 0.964

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4N7U

4n7u


Resolution: 1.2→45.04 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.953 / SU B: 0.898 / SU ML: 0.041 / Cross valid method: THROUGHOUT / ESU R: 0.05 / ESU R Free: 0.053 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23186 2743 4.9 %RANDOM
Rwork0.20278 ---
obs0.20425 52887 98.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 18.21 Å2
Baniso -1Baniso -2Baniso -3
1--0.67 Å20 Å20 Å2
2---0.67 Å20 Å2
3---1.33 Å2
Refinement stepCycle: 1 / Resolution: 1.2→45.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1513 0 0 308 1821
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0191584
X-RAY DIFFRACTIONr_bond_other_d0.0010.021485
X-RAY DIFFRACTIONr_angle_refined_deg1.7211.9582158
X-RAY DIFFRACTIONr_angle_other_deg0.82533441
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.3685196
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.69924.18974
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.31615266
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.781159
X-RAY DIFFRACTIONr_chiral_restr0.1240.2232
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.0211788
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02359
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_it1.9731.502769
X-RAY DIFFRACTIONr_mcbond_other1.9581.498768
X-RAY DIFFRACTIONr_mcangle_it2.5842.262964
X-RAY DIFFRACTIONr_mcangle_other2.5892.266965
X-RAY DIFFRACTIONr_scbond_it2.9611.768815
X-RAY DIFFRACTIONr_scbond_other2.9461.762813
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.2892.5411192
X-RAY DIFFRACTIONr_long_range_B_refined6.214.5222026
X-RAY DIFFRACTIONr_long_range_B_other5.98713.3371853
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.203→1.234 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.34 178 -
Rwork0.306 3793 -
obs--97.38 %

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