+Open data
-Basic information
Entry | Database: PDB / ID: 7s8j | ||||||
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Title | PHOSPHOPEPTIDE-SPECIFIC LC13 TCR, ORTHORHOMBIC CRYSTAL FORM | ||||||
Components |
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Keywords | IMMUNE SYSTEM / HLA / MLL PEPTIDE / HLA-B*07:02 / HLA-B7 / IMMUNITY / PHOSPHOPEPTIDE / CANCER / NEOANTIGEN / TCR | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.92 Å | ||||||
Authors | Patskovska, L. / Patskovsky, Y. / Nyovanie, S. / Natarajan, A. / Joshi, B. / Morin, B. / Brittsan, C. / Huber, O. / Gordon, S. / Michelet, X. ...Patskovska, L. / Patskovsky, Y. / Nyovanie, S. / Natarajan, A. / Joshi, B. / Morin, B. / Brittsan, C. / Huber, O. / Gordon, S. / Michelet, X. / Schmitzberger, F. / Stein, R. / Findeis, M. / Hurwitz, A. / Van Dijk, M. / Buell, J. / Underwood, D. / Krogsgaard, M. | ||||||
Funding support | United States, 1items
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Citation | Journal: Nat Commun / Year: 2023 Title: Molecular mechanism of phosphopeptide neoantigen immunogenicity. Authors: Patskovsky, Y. / Natarajan, A. / Patskovska, L. / Nyovanie, S. / Joshi, B. / Morin, B. / Brittsan, C. / Huber, O. / Gordon, S. / Michelet, X. / Schmitzberger, F. / Stein, R.B. / Findeis, M.A. ...Authors: Patskovsky, Y. / Natarajan, A. / Patskovska, L. / Nyovanie, S. / Joshi, B. / Morin, B. / Brittsan, C. / Huber, O. / Gordon, S. / Michelet, X. / Schmitzberger, F. / Stein, R.B. / Findeis, M.A. / Hurwitz, A. / Van Dijk, M. / Chantzoura, E. / Yague, A.S. / Pollack Smith, D. / Buell, J.S. / Underwood, D. / Krogsgaard, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7s8j.cif.gz | 114.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7s8j.ent.gz | 84.9 KB | Display | PDB format |
PDBx/mmJSON format | 7s8j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7s8j_validation.pdf.gz | 432.2 KB | Display | wwPDB validaton report |
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Full document | 7s8j_full_validation.pdf.gz | 434.6 KB | Display | |
Data in XML | 7s8j_validation.xml.gz | 22.3 KB | Display | |
Data in CIF | 7s8j_validation.cif.gz | 33.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/s8/7s8j ftp://data.pdbj.org/pub/pdb/validation_reports/s8/7s8j | HTTPS FTP |
-Related structure data
Related structure data | 7rzdC 7rzjC 7s79C 7s7dC 7s7eC 7s7fC 7s8aC 7s8eC 7s8fC 7s8iSC S: Starting model for refinement C: citing same article (ref.) |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 22647.143 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: PET30A / Production host: Escherichia coli BL21 (bacteria) | ||||
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#2: Protein | Mass: 27649.025 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: PET30A / Production host: Escherichia coli BL21(DE3) (bacteria) | ||||
#3: Chemical | ChemComp-CL / #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.43 Å3/Da / Density % sol: 49.48 % / Description: PLATE |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 5.6 Details: 20-25% PEG4000, 0.2M AMMONIUM, SULFATE, 0.1M SODIUM CITRATE, PH 5.6 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.9793 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 4, 2020 / Details: SI 111 CRYSTAL |
Radiation | Monochromator: SI 111 CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 1.92→29.21 Å / Num. obs: 37831 / % possible obs: 99.6 % / Redundancy: 5.6 % / Rmerge(I) obs: 0.087 / Net I/σ(I): 11.4 |
Reflection shell | Resolution: 1.92→1.97 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.695 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 2424 / % possible all: 95.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7S8I Resolution: 1.92→29.21 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.946 / SU B: 3.535 / SU ML: 0.101 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.142 / ESU R Free: 0.136 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 139.53 Å2 / Biso mean: 34.962 Å2 / Biso min: 16.05 Å2
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Refinement step | Cycle: final / Resolution: 1.92→29.21 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.924→1.974 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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