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- PDB-8dfx: Crystal structure of Human BTN2A1-BTN3A1 Ectodomain Complex -

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Basic information

Entry
Database: PDB / ID: 8dfx
TitleCrystal structure of Human BTN2A1-BTN3A1 Ectodomain Complex
Components
  • Butyrophilin subfamily 2 member A1
  • Butyrophilin subfamily 3 member A1
KeywordsIMMUNE SYSTEM / butyrophilins / T cells
Function / homology
Function and homology information


Butyrophilin (BTN) family interactions / activated T cell proliferation / regulation of cytokine production / positive regulation of cytokine production / lipid metabolic process / positive regulation of type II interferon production / T cell receptor signaling pathway / adaptive immune response / external side of plasma membrane / signaling receptor binding / plasma membrane
Similarity search - Function
Butyrophilin subfamily 1/2, SPRY/PRY domain / Butyrophilin subfamily 3, PRY/SPRY domain / SPRY-associated domain / SPRY-associated / PRY / Butyrophylin-like, SPRY domain / SPRY domain / B30.2/SPRY domain / B30.2/SPRY domain profile. / SPRY domain ...Butyrophilin subfamily 1/2, SPRY/PRY domain / Butyrophilin subfamily 3, PRY/SPRY 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 3 member A1 / Butyrophilin subfamily 2 member A1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 5.55 Å
AuthorsFulford, T.S. / Soliman, C. / Castle, R.G. / Rigau, M. / Ruan, Z. / Dolezal, O. / Seneviratna, R. / Brown, H.G. / Hanssen, E. / Hammet, A. ...Fulford, T.S. / Soliman, C. / Castle, R.G. / Rigau, M. / Ruan, Z. / Dolezal, O. / Seneviratna, R. / Brown, H.G. / Hanssen, E. / Hammet, A. / Li, S. / Redmond, S.J. / Chung, A. / Gorman, M.A. / Parker, M.W. / Patel, O. / Peat, T.S. / Newman, J. / Behren, A. / Gherardin, N.A. / Godfrey, D.I. / Uldrich, A.P.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)1184906 Australia
CitationJournal: To Be Published
Title: Vgamma9-Vdelta2 T cells recognize butyrophilin 2A1 and 3A1 heteromers
Authors: Fulford, T.S. / Soliman, C. / Castle, R.G. / Rigau, M. / Ruan, Z. / Dolezal, O. / Seneviratna, R. / Brown, H.G. / Hanssen, E. / Hammet, A. / Li, S. / Redmond, S.J. / Chung, A. / Gorman, M.A. ...Authors: Fulford, T.S. / Soliman, C. / Castle, R.G. / Rigau, M. / Ruan, Z. / Dolezal, O. / Seneviratna, R. / Brown, H.G. / Hanssen, E. / Hammet, A. / Li, S. / Redmond, S.J. / Chung, A. / Gorman, M.A. / Parker, M.W. / Patel, O. / Peat, T.S. / Newman, J. / Behren, A. / Gherardin, N.A. / Godfrey, D.I. / Uldrich, A.P.
History
DepositionJun 22, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 5, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Butyrophilin subfamily 2 member A1
B: Butyrophilin subfamily 3 member A1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,8923
Polymers58,4682
Non-polymers4241
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: surface plasmon resonance, fluorescence resonance energy transfer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)114.630, 138.930, 336.200
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number22
Space group name H-MF222

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Components

#1: Protein Butyrophilin subfamily 2 member A1


Mass: 25426.893 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BTN2A1, BT2.1, BTF1 / Cell line (production host): Expi293F GnTI- / Production host: Homo sapiens (human) / References: UniProt: Q7KYR7
#2: Protein Butyrophilin subfamily 3 member A1


Mass: 33041.191 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BTN3A1, BTF5 / Cell line (production host): Expi293F GnTI- / Production host: Homo sapiens (human) / References: UniProt: O00481
#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
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: 5.16 Å3/Da / Density % sol: 76 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 6% PEG 6000, 0.1 M magnesium sulfate, 0.1 M HEPES

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 23, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 5.55→47.4 Å / Num. obs: 2500 / % possible obs: 85.9 % / Redundancy: 7.4 % / Biso Wilson estimate: 273.78 Å2 / CC1/2: 0.919 / Rpim(I) all: 0.086 / Net I/σ(I): 5.3
Reflection shellResolution: 5.55→6.62 Å / Redundancy: 7.6 % / Mean I/σ(I) obs: 1.6 / Num. unique obs: 278 / CC1/2: 0.373 / Rpim(I) all: 0.558 / % possible all: 49.2

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
STARANISOdata scaling
PHASERphasing
BUSTER2.10.4 (3-FEB-2022)refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4F80, BTN2A1

4f80


Resolution: 5.55→47.35 Å / Cor.coef. Fo:Fc: 0.747 / Cor.coef. Fo:Fc free: 0.696 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 2.553
RfactorNum. reflection% reflectionSelection details
Rfree0.3361 226 9.04 %RANDOM
Rwork0.2899 ---
obs0.2942 2500 56.5 %-
Displacement parametersBiso mean: 277.95 Å2
Baniso -1Baniso -2Baniso -3
1-118.3093 Å20 Å20 Å2
2--139.4462 Å20 Å2
3----257.7555 Å2
Refine analyzeLuzzati coordinate error obs: 0.87 Å
Refinement stepCycle: LAST / Resolution: 5.55→47.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3277 0 28 0 3305
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0073380HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.914584HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1556SINUSOIDAL5
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes572HARMONIC5
X-RAY DIFFRACTIONt_it3350HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.05
X-RAY DIFFRACTIONt_other_torsion2.17
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion443SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2407SEMIHARMONIC4
LS refinement shellResolution: 5.55→6.52 Å / Total num. of bins used: 12
RfactorNum. reflection% reflection
Rfree0.3071 -10.09 %
Rwork0.2954 205 -
all0.2966 228 -
obs--13.58 %
Refinement TLS params.

L11: 16.6309 °2 / L22: 16.6309 °2 / L23: 5.8208 °2 / L33: 16.6309 °2 / S12: 1.0885 Å ° / S13: 1.0885 Å ° / S21: -1.0885 Å ° / S31: -1.0885 Å ° / S32: -1.0885 Å ° / T13: -0.304 Å2 / Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL12 (°2)L13 (°2)S11 (Å °)S22 (Å °)S23 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
1-5.8208-5.82080-1.08851.08851.08850.31820.304-0-0.304-0.540812.5303-15.6897-25.962
25.82085.82080.5627-0.52580.2483-0.03690.5457-0.304-0.60790.304046.1571-11.5456-21.6489
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }

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