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- PDB-9ln2: Crystal Structure of Intracellular B30.2 Domain of VpBTN3 in Comp... -

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Basic information

Entry
Database: PDB / ID: 9ln2
TitleCrystal Structure of Intracellular B30.2 Domain of VpBTN3 in Complex with DMASPP
ComponentsButyrophylin 3
KeywordsSIGNALING PROTEIN / Butyrophilin
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 3, PRY/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 ...Butyrophilin subfamily 3, PRY/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 / Immunoglobulin-like fold
Similarity search - Domain/homology
DIMETHYLALLYL S-THIOLODIPHOSPHATE / Butyrophylin 3
Similarity search - Component
Biological speciesVicugna pacos (alpaca)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.77 Å
AuthorsYang, Y.Y. / Yi, S.M. / Zhang, M.T. / Chen, C.-C. / Guo, R.-T.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)82271887 China
CitationJournal: J.Biol.Chem. / Year: 2025
Title: Molecular glue binding behavior of phosphoantigens to alpaca butyrophilins.
Authors: Liu, C. / Yi, S. / Zhang, M. / Chen, C.C. / Liu, Y. / Zhang, Z. / Guo, R.T. / Yang, Y.
History
DepositionJan 20, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0May 14, 2025Provider: repository / Type: Initial release
Revision 1.1Sep 3, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Butyrophylin 3
B: Butyrophylin 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,4418
Polymers53,7322
Non-polymers7086
Water7,927440
1
A: Butyrophylin 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,2505
Polymers26,8661
Non-polymers3844
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area330 Å2
ΔGint-24 kcal/mol
Surface area9370 Å2
MethodPISA
2
B: Butyrophylin 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,1903
Polymers26,8661
Non-polymers3242
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area440 Å2
ΔGint-5 kcal/mol
Surface area9350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.858, 67.988, 134.307
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 Butyrophylin 3


Mass: 26866.045 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
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-DST / DIMETHYLALLYL S-THIOLODIPHOSPHATE / DMASPP / DMAPP / DMADP / Dimethylallyl pyrophosphate / dimethylallyl diphosphate / isoprenyl pyrophosphate


Mass: 262.158 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H12O6P2S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 440 / 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: 1.86 Å3/Da / Density % sol: 33.99 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Bis Tris pH5.5, 2.0 M ammonium sulfate

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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: Jul 29, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.34138 Å / Relative weight: 1
ReflectionResolution: 1.77→36.75 Å / Num. obs: 39950 / % possible obs: 99.6 % / Redundancy: 11.5 % / Rmerge(I) obs: 0.046 / Net I/σ(I): 31.9
Reflection shellResolution: 1.77→1.8 Å / Rmerge(I) obs: 0.168 / Num. unique obs: 1878

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
SAINTdata reduction
SAINTdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.77→36.75 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.947 / SU B: 2.216 / SU ML: 0.07 / Cross valid method: THROUGHOUT / ESU R: 0.111 / ESU R Free: 0.112 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20163 1959 4.9 %RANDOM
Rwork0.15722 ---
obs0.15937 37867 99.45 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.646 Å2
Baniso -1Baniso -2Baniso -3
1-0.98 Å20 Å20 Å2
2---0.22 Å20 Å2
3----0.76 Å2
Refinement stepCycle: 1 / Resolution: 1.77→36.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3096 0 38 440 3574
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0133238
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172849
X-RAY DIFFRACTIONr_angle_refined_deg1.7071.6544418
X-RAY DIFFRACTIONr_angle_other_deg1.4581.5756619
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6275382
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.92621.848184
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.91715499
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.6571523
X-RAY DIFFRACTIONr_chiral_restr0.0850.2398
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.023612
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02729
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_it1.521.6121531
X-RAY DIFFRACTIONr_mcbond_other1.5031.6111530
X-RAY DIFFRACTIONr_mcangle_it2.2822.4091912
X-RAY DIFFRACTIONr_mcangle_other2.2842.4111913
X-RAY DIFFRACTIONr_scbond_it2.7621.9421707
X-RAY DIFFRACTIONr_scbond_other2.7611.9431708
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.2482.8012507
X-RAY DIFFRACTIONr_long_range_B_refined5.79719.9283738
X-RAY DIFFRACTIONr_long_range_B_other5.79719.9363739
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.77→1.816 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.266 149 -
Rwork0.206 2646 -
obs--95.56 %

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