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- PDB-5zxk: Crystal structure of intracellular B30.2 domain of BTN3A1 in comp... -

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Basic information

Entry
Database: PDB / ID: 5zxk
TitleCrystal structure of intracellular B30.2 domain of BTN3A1 in complex with HMBPP
ComponentsButyrophilin subfamily 3 member A1
KeywordsSIGNALING PROTEIN / substrate binding / agonist
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 / Immunoglobulin-like domain superfamily / Jelly Rolls / Immunoglobulin-like fold / Sandwich / Mainly Beta
Similarity search - Domain/homology
Chem-H6P / Butyrophilin subfamily 3 member A1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.96 Å
AuthorsYang, Y.Y. / 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 21, 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 A1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,9242
Polymers22,6621
Non-polymers2621
Water2,234124
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 area9240 Å2
Unit cell
Length a, b, c (Å)45.131, 125.668, 39.046
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Butyrophilin subfamily 3 member A1


Mass: 22661.773 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 328-513
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: Chemical ChemComp-H6P / (2E)-4-hydroxy-3-methylbut-2-en-1-yl trihydrogen diphosphate


Mass: 262.092 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H12O8P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 124 / 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: 2.44 Å3/Da / Density % sol: 49.65 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: CALCIUM ACETATE HYDRATE, PEG8000, SODIUM CACODYLATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13C1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 10, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.96→25 Å / Num. obs: 16009 / % possible obs: 96.9 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.084 / Net I/σ(I): 17.99
Reflection shellResolution: 1.96→2.08 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.409 / % possible all: 96.6

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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: 1.96→25 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.896 / SU B: 4.351 / SU ML: 0.122 / Cross valid method: THROUGHOUT / ESU R: 0.185 / ESU R Free: 0.178 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.265 797 5 %RANDOM
Rwork0.206 ---
obs0.209 15176 96.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 22.02 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2---0.08 Å20 Å2
3---0.07 Å2
Refinement stepCycle: LAST / Resolution: 1.96→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1507 0 15 124 1646
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0191591
X-RAY DIFFRACTIONr_bond_other_d0.0020.021473
X-RAY DIFFRACTIONr_angle_refined_deg1.9721.9512172
X-RAY DIFFRACTIONr_angle_other_deg1.0192.9933413
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5655193
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.67623.91974
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.95815261
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.338159
X-RAY DIFFRACTIONr_chiral_restr0.1070.2230
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0211777
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02366
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_it1.81.991754
X-RAY DIFFRACTIONr_mcbond_other1.7941.99753
X-RAY DIFFRACTIONr_mcangle_it2.6152.975944
X-RAY DIFFRACTIONr_mcangle_other2.6162.977945
X-RAY DIFFRACTIONr_scbond_it2.5372.278837
X-RAY DIFFRACTIONr_scbond_other2.5272.273830
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.9393.3091226
X-RAY DIFFRACTIONr_long_range_B_refined5.16616.5761863
X-RAY DIFFRACTIONr_long_range_B_other5.06516.4281829
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.96→2.01 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.263 43 -
Rwork0.237 982 -
obs--87.83 %

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