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- PDB-8dfw: Crystal Structure of Human BTN2A1 in Complex With Vgamma9-Vdelta2... -

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Basic information

Entry
Database: PDB / ID: 8dfw
TitleCrystal Structure of Human BTN2A1 in Complex With Vgamma9-Vdelta2 T Cell Receptor
Components
  • (T cell receptor ...) x 2
  • Butyrophilin subfamily 2 member A1
KeywordsIMMUNE SYSTEM / butyrophilins / T cells
Function / homology
Function and homology information


Butyrophilin (BTN) family interactions / regulation of cytokine production / lipid metabolic process / 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 A1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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
Remark 0 : statistics at the very beginning when nothing is done yet

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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 2 member A1
D: T cell receptor delta variable chain
G: T cell receptor gamma variable chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,31511
Polymers105,6714
Non-polymers2,6447
Water2,972165
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: surface plasmon resonance
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)112.030, 218.460, 107.930
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11B-424-

HOH

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Components

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T cell receptor ... , 2 types, 2 molecules DG

#2: Protein T cell receptor delta variable chain


Mass: 26488.951 Da / Num. of mol.: 1 / Mutation: C94S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TRDV2, TRDC / Cell line (production host): Expi293F GnTI- / Production host: Homo sapiens (human)
#3: Protein T cell receptor gamma variable chain


Mass: 28328.275 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TRGV9, TRGC1 / Cell line (production host): Expi293F GnTI- / Production host: Homo sapiens (human)

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Protein / Non-polymers , 2 types, 167 molecules AB

#1: Protein Butyrophilin subfamily 2 member A1


Mass: 25426.893 Da / Num. of mol.: 2
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
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 165 / Source method: isolated from a natural source / Formula: H2O

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Sugars , 4 types, 7 molecules

#4: Polysaccharide alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-6DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a4-b1_b4-c1_c6-d1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(6+1)][a-D-Manp]{}}}}LINUCSPDB-CARE
#5: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}LINUCSPDB-CARE
#6: 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-ROHGlycam 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
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#7: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Details

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: 3.13 Å3/Da / Density % sol: 61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 20% PEG 3350, 0.2 M sodium malonate-malonic acid

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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: 2.1→49.72 Å / Num. obs: 77369 / % possible obs: 99.97 % / Redundancy: 13.4 % / Biso Wilson estimate: 39.16 Å2 / CC1/2: 0.998 / Rpim(I) all: 0.0337 / Net I/σ(I): 13.78
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 13.8 % / Mean I/σ(I) obs: 2.84 / Num. unique obs: 3834 / CC1/2: 0.725 / Rpim(I) all: 0.299 / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTER2.10.4 (11-DEC-2020)refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1HXM, BTN2A1

1hxm


Resolution: 2.1→49.72 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.914 / SU R Cruickshank DPI: 0.21 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.206 / SU Rfree Blow DPI: 0.179 / SU Rfree Cruickshank DPI: 0.183
RfactorNum. reflection% reflectionSelection details
Rfree0.2866 3723 4.81 %RANDOM
Rwork0.2606 ---
obs0.2618 77362 100 %-
Displacement parametersBiso mean: 58.2 Å2
Baniso -1Baniso -2Baniso -3
1--5.0383 Å20 Å20 Å2
2--2.9899 Å20 Å2
3---2.0484 Å2
Refine analyzeLuzzati coordinate error obs: 0.36 Å
Refinement stepCycle: LAST / Resolution: 2.1→49.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6646 0 173 165 6984
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0087193HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.029769HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d3372SINUSOIDAL3.5
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes1199HARMONIC5
X-RAY DIFFRACTIONt_it7193HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.64
X-RAY DIFFRACTIONt_other_torsion2.61
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion997SEMIHARMONIC5
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_contact5356SEMIHARMONIC4
LS refinement shellResolution: 2.1→2.136 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.359 189 4.93 %
Rwork0.3358 3645 -
all0.337 3834 -
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.0962-0.4815-2.37990.24171.90024.00520.2784-0.62630.4559-0.35670.15220.00490.02780.8041-0.4306-0.09930.02560.02160.1949-0.18660.05259.633826.137-12.7781
24.39450.96711.904300.11611.23970.0076-0.5714-0.0697-0.001-0.1178-0.0002-0.1517-0.1420.11020.08470.1375-0.13610.144-0.0792-0.031845.61838.2951-21.4231
30-1.4622-0.01824.89390.30650.7098-0.0054-0.2492-0.1014-0.02490.15510.60290.00750.1226-0.1497-0.2337-0.00570.1274-0.0309-0.13670.3271-37.081543.745920.5119
40-2.1053-0.89222.98811.1261.7597-0.0152-0.34620.4959-0.13420.7832-0.57710.07460.4064-0.768-0.36850.01240.09490.0753-0.3040.483-18.614441.34819.5735
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ D|* }
4X-RAY DIFFRACTION4{ G|* }

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