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- PDB-8ih4: Crystal Structure of Intracellular B30.2 Domain of BTN2A2 Mutant -

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Basic information

Entry
Database: PDB / ID: 8ih4
TitleCrystal Structure of Intracellular B30.2 Domain of BTN2A2 Mutant
ComponentsButyrophilin subfamily 2 member A2
KeywordsSIGNALING PROTEIN / Butyrophilin
Function / homology
Function and homology information


: / : / Butyrophilin (BTN) family interactions / positive regulation of regulatory T cell differentiation / negative regulation of cytokine production / negative regulation of T cell receptor signaling pathway / negative regulation of G1/S transition of mitotic cell cycle / negative regulation of activated T cell proliferation / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / regulation of cytokine production ...: / : / Butyrophilin (BTN) family interactions / positive regulation of regulatory T cell differentiation / negative regulation of cytokine production / negative regulation of T cell receptor signaling pathway / negative regulation of G1/S transition of mitotic cell cycle / negative regulation of activated T cell proliferation / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / regulation of cytokine production / ERK1 and ERK2 cascade / phosphatidylinositol 3-kinase/protein kinase B signal transduction / negative regulation of ERK1 and ERK2 cascade / G1/S transition of mitotic cell cycle / T cell receptor signaling pathway / external side of plasma membrane / signaling receptor binding / plasma membrane
Similarity search - Function
Butyrophilin subfamily 1/2, SPRY/PRY 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 ...Butyrophilin subfamily 1/2, SPRY/PRY 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 / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Butyrophilin subfamily 2 member A2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.12 Å
AuthorsYang, Y.Y. / Yi, S.M. / Zhang, M.T. / Chen, C.C. / Guo, R.T. / Zhang, Y.H.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) 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
DepositionFeb 22, 2023Deposition 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Butyrophilin subfamily 2 member A2
B: Butyrophilin subfamily 2 member A2


Theoretical massNumber of molelcules
Total (without water)48,8232
Polymers48,8232
Non-polymers00
Water2,414134
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3920 Å2
ΔGint-14 kcal/mol
Surface area17760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.673, 59.843, 127.612
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Butyrophilin subfamily 2 member A2


Mass: 24411.643 Da / Num. of mol.: 2 / Mutation: W374R, M506T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BTN2A2, BT2.2, BTF2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8WVV5
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 134 / 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: 2.18 Å3/Da / Density % sol: 43.5 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 0.2 M sodium citrate tribasic dihydrate, 20% w/v polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: LIQUID ANODE / Type: BRUKER METALJET / Wavelength: 1.34 Å
DetectorType: Bruker PHOTON III / Detector: PIXEL / Date: Apr 25, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.34 Å / Relative weight: 1
ReflectionResolution: 2.12→29.94 Å / Num. obs: 24957 / % possible obs: 99.9 % / Redundancy: 9.62 % / Rmerge(I) obs: 0.1057 / Net I/σ(I): 11.6
Reflection shellResolution: 2.12→2.15 Å / Rmerge(I) obs: 0.4876 / Num. unique obs: 1012

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
SADABSdata scaling
PDB_EXTRACT3.27data extraction
Cootmodel building
PHASERphasing
SAINTdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ZXK

5zxk


Resolution: 2.12→29.94 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.916 / SU B: 6.93 / SU ML: 0.171 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.251 / ESU R Free: 0.211 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2603 1227 4.9 %RANDOM
Rwork0.2042 ---
obs0.2071 23654 99.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 104.9 Å2 / Biso mean: 36.295 Å2 / Biso min: 17.71 Å2
Baniso -1Baniso -2Baniso -3
1-2.43 Å20 Å20 Å2
2---0.74 Å20 Å2
3----1.69 Å2
Refinement stepCycle: final / Resolution: 2.12→29.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3158 0 0 134 3292
Biso mean---35.8 -
Num. residues----392
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0133297
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172995
X-RAY DIFFRACTIONr_angle_refined_deg1.5451.6534485
X-RAY DIFFRACTIONr_angle_other_deg1.221.5736917
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.1985400
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.14119.423208
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.81715523
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5861541
X-RAY DIFFRACTIONr_chiral_restr0.0640.2398
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023764
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02807
LS refinement shellResolution: 2.12→2.175 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.303 99 -
Rwork0.286 1697 -
all-1796 -
obs--99.83 %

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