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- PDB-6j0k: Crystal structure of intracellular B30.2 domain of BTN3A3 mutant ... -

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Basic information

Entry
Database: PDB / ID: 6j0k
TitleCrystal structure of intracellular B30.2 domain of BTN3A3 mutant in complex with HMBPP
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 / external side of plasma membrane / signaling receptor binding / membrane / plasma membrane
Similarity search - Function
Butyrophilin subfamily 3, PRY/SPRY domain / SPRY domain / SPRY-associated domain / SPRY-associated / PRY / Butyrophylin-like, SPRY domain / SPRY domain / B30.2/SPRY domain / B30.2/SPRY domain profile. / SPRY domain ...Butyrophilin subfamily 3, PRY/SPRY domain / SPRY domain / SPRY-associated domain / SPRY-associated / PRY / Butyrophylin-like, SPRY domain / SPRY domain / B30.2/SPRY domain / B30.2/SPRY domain profile. / SPRY domain / B30.2/SPRY domain superfamily / Domain in SPla and the RYanodine Receptor. / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Concanavalin A-like lectin/glucanase domain superfamily / Immunoglobulin subtype / Immunoglobulin / Jelly Rolls / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Sandwich / Mainly Beta
Similarity search - Domain/homology
Chem-H6P / Butyrophilin subfamily 3 member A3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 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
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

Downloads & links

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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)51,0694
Polymers50,5452
Non-polymers5242
Water3,279182
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Butyrophilin subfamily 3 member A3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,5352
Polymers25,2721
Non-polymers2621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.797, 41.392, 62.490
Angle α, β, γ (deg.)73.23, 89.87, 68.95
Int Tables number1
Space group name H-MP1

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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-H6P / (2E)-4-hydroxy-3-methylbut-2-en-1-yl trihydrogen diphosphate / (E)-4-Hydroxy-3-methyl-but-2-enyl pyrophosphate


Mass: 262.092 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H12O8P2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 182 / 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: 1.76 Å3/Da / Density % sol: 30.22 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: Isopropanol ,Imidazole, PEG 8000

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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 29, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→25 Å / Num. obs: 20422 / % possible obs: 84.2 % / Redundancy: 3 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 16.06
Reflection shellResolution: 2→2.07 Å / Num. unique obs: 2264 / CC1/2: 0.946

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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: 2→25 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.912 / SU B: 4.815 / SU ML: 0.139 / Cross valid method: THROUGHOUT / ESU R: 0.299 / ESU R Free: 0.226 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25662 997 4.9 %RANDOM
Rwork0.19091 ---
obs0.1942 19413 81.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 25.298 Å2
Baniso -1Baniso -2Baniso -3
1--0.31 Å20.67 Å2-0.14 Å2
2---0.36 Å21.33 Å2
3---1.96 Å2
Refinement stepCycle: 1 / Resolution: 2→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3102 0 30 182 3314
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0193245
X-RAY DIFFRACTIONr_bond_other_d0.0010.022953
X-RAY DIFFRACTIONr_angle_refined_deg1.1741.9584430
X-RAY DIFFRACTIONr_angle_other_deg0.63536833
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.215386
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.17223.503157
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.88615509
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.5291522
X-RAY DIFFRACTIONr_chiral_restr0.0760.2458
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0213621
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02753
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_it2.6022.3581532
X-RAY DIFFRACTIONr_mcbond_other2.6022.3561531
X-RAY DIFFRACTIONr_mcangle_it3.2733.5171913
X-RAY DIFFRACTIONr_mcangle_other3.2723.5191914
X-RAY DIFFRACTIONr_scbond_it3.2272.6411713
X-RAY DIFFRACTIONr_scbond_other3.2262.6411714
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.4973.8642515
X-RAY DIFFRACTIONr_long_range_B_refined5.44519.5113799
X-RAY DIFFRACTIONr_long_range_B_other5.44419.5143800
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.954→2.005 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.281 65 -
Rwork0.224 984 -
obs--57.51 %

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