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

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Basic information

Entry
Database: PDB / ID: 6ism
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 / : / : / 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 A1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 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 16, 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)22,5051
Polymers22,5051
Non-polymers00
Water4,017223
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 area9140 Å2
Unit cell
Length a, b, c (Å)47.029, 54.305, 63.027
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Butyrophilin subfamily 3 member A1


Mass: 22504.562 Da / Num. of mol.: 1 / Fragment: UNP residues 328-513 / Mutation: W302A, L306A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BTN3A1, BTF5 / Production host: Escherichia coli (E. coli) / References: UniProt: O00481
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 223 / 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: 1.79 Å3/Da / Density % sol: 31.21 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: Magnesium chloride hexahydrate, HEPES pH 7.5, Polyethylene glycol monomethyl ether 550

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 1 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Oct 22, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.25→41.14 Å / Num. obs: 42394 / % possible obs: 97.99 % / Redundancy: 10.7 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 53.69
Reflection shellResolution: 1.25→1.29 Å / Rmerge(I) obs: 0.288 / Num. unique obs: 3880 / CC1/2: 0.914

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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: 1.25→41.14 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.959 / SU B: 0.709 / SU ML: 0.032 / Cross valid method: THROUGHOUT / ESU R: 0.05 / ESU R Free: 0.054 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20521 2155 4.8 %RANDOM
Rwork0.1736 ---
obs0.17513 42394 97.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 17.721 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å2-0 Å20 Å2
2---0.02 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 1.25→41.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1497 0 0 223 1720
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0191604
X-RAY DIFFRACTIONr_bond_other_d0.0010.021498
X-RAY DIFFRACTIONr_angle_refined_deg1.7171.9512194
X-RAY DIFFRACTIONr_angle_other_deg0.7933468
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.9345201
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.93523.51474
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.68915266
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1551511
X-RAY DIFFRACTIONr_chiral_restr0.1220.2234
X-RAY DIFFRACTIONr_gen_planes_refined0.0160.0211832
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02377
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_it1.9891.485777
X-RAY DIFFRACTIONr_mcbond_other1.9811.482776
X-RAY DIFFRACTIONr_mcangle_it2.8972.223981
X-RAY DIFFRACTIONr_mcangle_other2.8982.226982
X-RAY DIFFRACTIONr_scbond_it3.4031.786827
X-RAY DIFFRACTIONr_scbond_other3.4011.787828
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.8542.5451212
X-RAY DIFFRACTIONr_long_range_B_refined6.51213.8341960
X-RAY DIFFRACTIONr_long_range_B_other6.41613.0751838
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.249→1.282 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.252 138 -
Rwork0.245 2553 -
obs--81.03 %

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