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- PDB-8hjt: Crystal Structure of Intracellular B30.2 Domain of VpBTN3 and VpB... -

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Basic information

Entry
Database: PDB / ID: 8hjt
TitleCrystal Structure of Intracellular B30.2 Domain of VpBTN3 and VpBTN2 in Complex with HMBPP
Components
  • Butyrophylin 3
  • butyrophilin subfamily 2 member A2
KeywordsIMMUNE SYSTEM / Butyrophilin / Signaling Protein
Function / homology
Function and homology information


regulation of cytokine production / T cell receptor signaling pathway / signaling receptor binding / external side of plasma membrane
Similarity search - Function
Butyrophilin subfamily 1/2, SPRY/PRY 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 ...Butyrophilin subfamily 1/2, SPRY/PRY 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
Chem-H6P / Butyrophylin 3 / Butyrophilin subfamily 2 member A2
Similarity search - Component
Biological speciesVicugna pacos (alpaca)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.91 Å
AuthorsYang, Y.Y. / Shen, P.P. / Li, X. / Yi, S.M. / Zhang, M.T. / Huang, J.-W. / Chen, C.-C. / Guo, R.-T.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)82271887 China
CitationJournal: Nature / Year: 2023
Title: Phosphoantigens glue butyrophilin 3A1 and 2A1 to activate V gamma 9V delta 2 T cells.
Authors: Yuan, L. / Ma, X. / Yang, Y. / Qu, Y. / Li, X. / Zhu, X. / Ma, W. / Duan, J. / Xue, J. / Yang, H. / Huang, J.W. / Yi, S. / Zhang, M. / Cai, N. / Zhang, L. / Ding, Q. / Lai, K. / Liu, C. / ...Authors: Yuan, L. / Ma, X. / Yang, Y. / Qu, Y. / Li, X. / Zhu, X. / Ma, W. / Duan, J. / Xue, J. / Yang, H. / Huang, J.W. / Yi, S. / Zhang, M. / Cai, N. / Zhang, L. / Ding, Q. / Lai, K. / Liu, C. / Zhang, L. / Liu, X. / Yao, Y. / Zhou, S. / Li, X. / Shen, P. / Chang, Q. / Malwal, S.R. / He, Y. / Li, W. / Chen, C. / Chen, C.C. / Oldfield, E. / Guo, R.T. / Zhang, Y.
History
DepositionNov 23, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 13, 2023Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: Database references / Category: citation / citation_author / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Oct 11, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 18, 2023Group: Database references / Category: citation_author / Item: _citation_author.identifier_ORCID
Revision 1.4Nov 27, 2024Group: Refinement description / Structure summary
Category: pdbx_entry_details / pdbx_initial_refinement_model
Item: _pdbx_entry_details.has_protein_modification / _pdbx_initial_refinement_model.accession_code ..._pdbx_entry_details.has_protein_modification / _pdbx_initial_refinement_model.accession_code / _pdbx_initial_refinement_model.source_name / _pdbx_initial_refinement_model.type

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: butyrophilin subfamily 2 member A2
B: butyrophilin subfamily 2 member A2
C: Butyrophylin 3
D: Butyrophylin 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,5737
Polymers97,8104
Non-polymers7623
Water2,018112
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)78.188, 78.188, 299.827
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z

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Components

#1: Protein butyrophilin subfamily 2 member A2


Mass: 26422.887 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vicugna pacos (alpaca) / Gene: LOC102538576 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A6J0B3M7
#2: Protein Butyrophylin 3


Mass: 22482.258 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vicugna pacos (alpaca) / Gene: Btn3 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A345DF50
#3: Chemical ChemComp-H6P / (2E)-4-hydroxy-3-methylbut-2-en-1-yl trihydrogen diphosphate


Mass: 262.092 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H12O8P2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 112 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.7 Å3/Da / Density % sol: 54.53 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / Details: 12% PEG 8k, 0.1 M HEPES pH7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: LIQUID ANODE / Type: BRUKER METALJET / Wavelength: 1.34138 Å
DetectorType: Bruker PHOTON III / Detector: PIXEL / Date: Sep 27, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.34138 Å / Relative weight: 1
ReflectionResolution: 2.91→35 Å / Num. obs: 24182 / % possible obs: 99.1 % / Redundancy: 7.1 % / Biso Wilson estimate: 37.11 Å2 / CC1/2: 1 / Net I/σ(I): 16.9
Reflection shellResolution: 2.91→2.96 Å / Num. unique obs: 1131 / CC1/2: 0.96

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
SAINTdata reduction
SAINTdata scaling
PHASERphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.91→34.66 Å / SU ML: 0.4087 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 25.9585
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2741 1154 4.95 %
Rwork0.2218 22151 -
obs0.2244 23305 95.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 36.64 Å2
Refinement stepCycle: LAST / Resolution: 2.91→34.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6024 0 45 112 6181
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00236247
X-RAY DIFFRACTIONf_angle_d0.5248508
X-RAY DIFFRACTIONf_chiral_restr0.045889
X-RAY DIFFRACTIONf_plane_restr0.00431119
X-RAY DIFFRACTIONf_dihedral_angle_d18.6942863
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.91-3.040.39471480.30552389X-RAY DIFFRACTION85.85
3.04-3.20.34761430.27932523X-RAY DIFFRACTION90.13
3.2-3.40.30771230.24582719X-RAY DIFFRACTION94.17
3.4-3.670.28711440.23152757X-RAY DIFFRACTION97.64
3.67-4.030.27031590.2092843X-RAY DIFFRACTION99.77
4.03-4.620.20771370.19192918X-RAY DIFFRACTION99.84
4.62-5.810.25751320.19242926X-RAY DIFFRACTION99.84
5.81-34.660.23991680.21813076X-RAY DIFFRACTION99.24

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