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Open data
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Basic information
Entry | Database: PDB / ID: 8dfy | ||||||
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Title | Crystal structure of Human BTN2A1 Ectodomain | ||||||
![]() | Butyrophilin subfamily 2 member A1 | ||||||
![]() | IMMUNE SYSTEM / butyrophilins / T cells | ||||||
Function / homology | ![]() 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 | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Fulford, 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 | ![]()
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![]() | ![]() 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 446.7 KB | Display | ![]() |
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PDB format | ![]() | 375.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.4 MB | Display | ![]() |
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Full document | ![]() | 2.4 MB | Display | |
Data in XML | ![]() | 41.2 KB | Display | |
Data in CIF | ![]() | 54.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8dfwC ![]() 8dfxC ![]() 4hh8S S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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3 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 25426.893 Da / Num. of mol.: 5 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #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 Source method: isolated from a genetically manipulated source #3: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #4: Sugar | ChemComp-NAG / Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 5.68 Å3/Da / Density % sol: 78 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 1.65 M ammonium sulfate, 2% v/v PEG 400, 0.1 M HEPES |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 29, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 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 shell | Resolution: 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
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Refinement | Method to determine structure: ![]() Starting model: 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
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Displacement parameters | Biso mean: 268.94 Å2
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Refine analyze | Luzzati coordinate error obs: 0.59 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.552→49.75 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.552→3.76 Å
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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