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- PDB-8igt: Crystal Structure of Intracellular B30.2 Domain of BTN2A1 -

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Basic information

Entry
Database: PDB / ID: 8igt
TitleCrystal Structure of Intracellular B30.2 Domain of BTN2A1
ComponentsButyrophilin subfamily 2 member A1
KeywordsSIGNALING PROTEIN / Butyrophilin
Function / homology
Function and homology information


Butyrophilin (BTN) family interactions / regulation of cytokine production / lipid metabolic process / T cell receptor signaling pathway / signaling receptor binding / external side of plasma membrane / plasma membrane
Similarity search - Function
Butyrophilin subfamily 1/2, SPRY/PRY domain / : / : / Butyrophilin subfamily 3 member A2-like, Ig-C domain / SPRY domain / SPRY-associated domain / SPRY-associated / PRY / Butyrophylin-like, SPRY domain / SPRY domain ...Butyrophilin subfamily 1/2, SPRY/PRY 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
Butyrophilin subfamily 2 member A1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.56 Å
AuthorsYuan, L.J. / Yang, Y.Y. / Li, X. / Cai, N.N. / Chen, C.C. / Guo, R.T. / Zhang, Y.H.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32100711 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 21, 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 A1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,6172
Polymers25,5521
Non-polymers651
Water4,486249
1
A: Butyrophilin subfamily 2 member A1
hetero molecules

A: Butyrophilin subfamily 2 member A1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,2354
Polymers51,1042
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Buried area3860 Å2
ΔGint-11 kcal/mol
Surface area19740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.957, 78.889, 41.682
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Butyrophilin subfamily 2 member A1


Mass: 25551.893 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BTN2A1, BT2.1, BTF1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q7KYR7
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 249 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.38 Å3/Da / Density % sol: 48.31 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / Details: 0.4 M potassium sodium tartrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 22, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.56→50 Å / Num. obs: 35687 / % possible obs: 99.6 % / Redundancy: 12.7 % / Rmerge(I) obs: 0.095 / Rpim(I) all: 0.027 / Rrim(I) all: 0.099 / Χ2: 0.741 / Net I/σ(I): 4.7 / Num. measured all: 454210
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.56-1.5910.10.47116470.9470.1510.4950.49793.5
1.59-1.6212.60.43517840.9670.1260.4530.502100
1.62-1.65130.40717570.9740.1160.4240.523100
1.65-1.6813.20.38617430.9730.1090.4020.532100
1.68-1.7213.10.34517740.9780.0980.3590.553100
1.72-1.7612.80.29417500.9830.0850.3060.577100
1.76-1.812.20.25817880.9850.0760.2690.617100
1.8-1.8512.80.22417500.9880.0640.2330.654100
1.85-1.913.40.21218000.9890.060.2210.685100
1.9-1.9713.40.19417360.9910.0550.2020.846100
1.97-2.0413.10.1517910.9930.0430.1560.808100
2.04-2.1212.60.13517730.9940.0390.1410.873100
2.12-2.2112.30.12317880.9950.0360.1280.871100
2.21-2.3313.40.12617850.9950.0350.1311.003100
2.33-2.4813.30.10117960.9960.0290.1050.82100
2.48-2.67130.0917820.9970.0260.0940.836100
2.67-2.9412.40.07918190.9980.0230.0830.871100
2.94-3.3613.50.06818150.9980.0190.0710.924100
3.36-4.2312.30.05918540.9980.0170.0610.932100
4.23-5011.90.05219550.9980.0150.0540.78799.4

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
REFMAC5.8.0238refinement
PDB_EXTRACT3.27data extraction
Cootmodel building
PHASERphasing
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ZXK

5zxk


Resolution: 1.56→28.67 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.966 / SU B: 1.104 / SU ML: 0.04 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.067 / ESU R Free: 0.066 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1732 1768 5 %RANDOM
Rwork0.1549 ---
obs0.1558 33873 99.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 80.72 Å2 / Biso mean: 17.193 Å2 / Biso min: 8.28 Å2
Baniso -1Baniso -2Baniso -3
1--1.46 Å2-0 Å2-0 Å2
2--0.38 Å2-0 Å2
3---1.08 Å2
Refinement stepCycle: final / Resolution: 1.56→28.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1673 0 1 249 1923
Biso mean--21.6 29.82 -
Num. residues----208
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0131758
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171576
X-RAY DIFFRACTIONr_angle_refined_deg1.8241.6452396
X-RAY DIFFRACTIONr_angle_other_deg1.4831.5733652
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.755216
X-RAY DIFFRACTIONr_dihedral_angle_2_deg24.47820.092109
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.27615277
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7571519
X-RAY DIFFRACTIONr_chiral_restr0.0980.2214
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.022009
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02416
LS refinement shellResolution: 1.56→1.597 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.211 125 -
Rwork0.196 2378 -
obs--96.42 %

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