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- PDB-8dfy: Crystal structure of Human BTN2A1 Ectodomain -

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Basic information

Entry
Database: PDB / ID: 8dfy
TitleCrystal structure of Human BTN2A1 Ectodomain
ComponentsButyrophilin 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 / 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-associated domain / SPRY-associated / PRY / Butyrophylin-like, SPRY domain / SPRY domain / B30.2/SPRY domain ...Butyrophilin subfamily 1/2, SPRY/PRY 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
Butyrophilin subfamily 2 member A1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.552 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
Revision 1.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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
B: Butyrophilin subfamily 2 member A1
C: Butyrophilin subfamily 2 member A1
D: Butyrophilin subfamily 2 member A1
E: Butyrophilin subfamily 2 member A1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,31925
Polymers127,1345
Non-polymers7,18520
Water00
1
A: Butyrophilin subfamily 2 member A1
C: Butyrophilin subfamily 2 member A1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,71910
Polymers50,8542
Non-polymers2,8668
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Butyrophilin subfamily 2 member A1
hetero molecules

B: Butyrophilin subfamily 2 member A1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,35410
Polymers50,8542
Non-polymers2,5008
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
3
D: Butyrophilin subfamily 2 member A1
E: Butyrophilin subfamily 2 member A1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,92310
Polymers50,8542
Non-polymers3,0698
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)237.013, 94.189, 134.719
Angle α, β, γ (deg.)90.00, 106.34, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Butyrophilin subfamily 2 member A1


Mass: 25426.893 Da / Num. of mol.: 5
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: 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.: 7
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam 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
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#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
#4: 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.: 12
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
Has ligand of interestN
Has protein modificationY

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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: 5.68 Å3/Da / Density % sol: 78 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 1.65 M ammonium sulfate, 2% v/v PEG 400, 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: Sep 29, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 3.55→49.8 Å / Num. obs: 22300 / % possible obs: 85.2 % / Redundancy: 4.6 % / Biso Wilson estimate: 81.97 Å2 / CC1/2: 0.98 / Rpim(I) all: 0.108 / Net I/σ(I): 5.8
Reflection shellResolution: 3.55→3.89 Å / Redundancy: 5 % / Mean I/σ(I) obs: 2 / Num. unique obs: 1115 / CC1/2: 0.64 / Rpim(I) all: 0.513 / % possible all: 70

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Processing

Software
NameVersionClassification
BUSTER2.10.4 (11-DEC-2020)refinement
MOSFLMdata reduction
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4HH8

4hh8


Resolution: 3.552→49.75 Å / Cor.coef. Fo:Fc: 0.812 / Cor.coef. Fo:Fc free: 0.806 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.672
RfactorNum. reflection% reflectionSelection details
Rfree0.2679 1144 5.13 %RANDOM
Rwork0.2552 ---
obs0.2559 22300 64.4 %-
Displacement parametersBiso mean: 268.94 Å2
Baniso -1Baniso -2Baniso -3
1--2.5033 Å20 Å2-12.9171 Å2
2--3.4663 Å20 Å2
3----0.963 Å2
Refine analyzeLuzzati coordinate error obs: 0.59 Å
Refinement stepCycle: LAST / Resolution: 3.552→49.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8524 0 469 0 8993
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0089223HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.9912547HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d4335SINUSOIDAL4.5
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes1540HARMONIC5
X-RAY DIFFRACTIONt_it8719HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.94
X-RAY DIFFRACTIONt_other_torsion2.69
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1304SEMIHARMONIC5
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_contact6528SEMIHARMONIC4
LS refinement shellResolution: 3.552→3.76 Å
RfactorNum. reflection% reflection
Rfree0.4338 -5.16 %
Rwork0.3559 423 -
obs--8.3 %
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)
10.3529-0.0799-0.74610.1644-0.5320.985-0.2664-0.20570.2044-0.12970.2179-0.33320.1865-0.13670.04860.25280.0955-0.08430.121-0.0654-0.1065-7.982184.999461.7528
20.15560.7785-0.28111.3315-0.37920.1083-0.08240.0441-0.11180.1120.402-0.1019-0.1965-0.1634-0.31960.34580.0933-0.0222-0.07260.21340-11.066139.738215.5934
37.4129-0.82732.88212.1305-3.3583.52070.1995-0.8509-0.47470.3697-0.6422-0.5687-0.31070.46030.44260.39090.033-0.11120.32110.26120.081927.391873.486542.759
414.7576-5.037-4.236511.29882.51486.4059-0.0019-0.3880.5201-0.7619-0.58320.475-0.6412-0.81650.5852-0.39570.2249-0.07010.1180.31330.381185.952687.131525.6172
515.77527.2237-3.29384.3705-3.94754.48560.12310.5750.0008-0.36430.1862-0.6723-0.32140.1722-0.3093-0.1182-0.20070.1181-0.02190.20320.224849.137675.55432.0928
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ C|* }
4X-RAY DIFFRACTION4{ D|* }
5X-RAY DIFFRACTION5{ E|* }

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