+Open data
-Basic information
Entry | Database: PDB / ID: 6mnm | ||||||
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Title | 6256 TCR bound to I-Ab Padi4 | ||||||
Components |
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Keywords | IMMUNE SYSTEM / T cell receptor / Major Histocompatibility Complex | ||||||
Function / homology | Function and homology information positive regulation of antigen processing and presentation / positive regulation of alpha-beta T cell activation / Chromatin modifying enzymes / histone H3R2 arginine deiminase activity / histone H3R8 arginine deiminase activity / histone H3R17 arginine deiminase activity / histone arginine deiminase activity / histone H3R26 arginine deiminase activity / protein-arginine deiminase / protein-arginine deiminase activity ...positive regulation of antigen processing and presentation / positive regulation of alpha-beta T cell activation / Chromatin modifying enzymes / histone H3R2 arginine deiminase activity / histone H3R8 arginine deiminase activity / histone H3R17 arginine deiminase activity / histone arginine deiminase activity / histone H3R26 arginine deiminase activity / protein-arginine deiminase / protein-arginine deiminase activity / positive regulation of T-helper 1 type immune response / protein antigen binding / antigen processing and presentation of peptide antigen / B cell affinity maturation / positive regulation of T cell differentiation / stem cell population maintenance / response to type II interferon / antigen processing and presentation / toxic substance binding / post-translational protein modification / negative regulation of T cell proliferation / multivesicular body / cellular response to type II interferon / peptide antigen assembly with MHC class II protein complex / MHC class II protein complex / peptide antigen binding / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / positive regulation of T cell activation / nucleosome assembly / chromatin organization / MHC class II protein complex binding / late endosome membrane / adaptive immune response / early endosome / lysosome / chromatin remodeling / immune response / external side of plasma membrane / lysosomal membrane / innate immune response / ubiquitin protein ligase binding / calcium ion binding / protein-containing complex binding / cell surface / Golgi apparatus / protein-containing complex / identical protein binding / membrane / nucleus / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.1 Å | ||||||
Authors | Blevins, S.J. / Stadinski, B.D. / Huseby, E.S. | ||||||
Citation | Journal: Nat.Immunol. / Year: 2019 Title: A temporal thymic selection switch and ligand binding kinetics constrain neonatal Foxp3+Tregcell development. Authors: Stadinski, B.D. / Blevins, S.J. / Spidale, N.A. / Duke, B.R. / Huseby, P.G. / Stern, L.J. / Huseby, E.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6mnm.cif.gz | 170 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6mnm.ent.gz | 128.7 KB | Display | PDB format |
PDBx/mmJSON format | 6mnm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6mnm_validation.pdf.gz | 448.8 KB | Display | wwPDB validaton report |
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Full document | 6mnm_full_validation.pdf.gz | 455.6 KB | Display | |
Data in XML | 6mnm_validation.xml.gz | 28.2 KB | Display | |
Data in CIF | 6mnm_validation.cif.gz | 38.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mn/6mnm ftp://data.pdbj.org/pub/pdb/validation_reports/mn/6mnm | HTTPS FTP |
-Related structure data
Related structure data | 6mkdSC 6mkrC 6mngC 6mnnC 6mnoC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 20313.693 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: H2-Aa / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P14434 |
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#2: Protein | Mass: 25027.908 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Padi4, Pad4, Pdi4, H2-Ab1, H2-iabeta / Production host: Spodoptera frugiperda (fall armyworm) References: UniProt: Q9Z183, UniProt: P14483, protein-arginine deiminase |
#3: Protein | Mass: 23186.605 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pET30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) |
#4: Protein | Mass: 26756.602 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pET30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.11 Å3/Da / Density % sol: 60.47 % / Mosaicity: 0.13 ° |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.8 / Details: 14% PEG 4000, 100mM NaCacodylate, 100 mM NaCitrate |
-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 9M / Detector: PIXEL / Date: Aug 1, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 3.1→29.06 Å / Num. obs: 21458 / % possible obs: 99.9 % / Redundancy: 6.8 % / Biso Wilson estimate: 55.49 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.108 / Rpim(I) all: 0.045 / Rrim(I) all: 0.117 / Net I/σ(I): 11.5 |
Reflection shell | Resolution: 3.1→3.31 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.313 / Num. unique obs: 3884 / CC1/2: 0.983 / Rpim(I) all: 0.129 / Rrim(I) all: 0.339 / % possible all: 100 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6MKD Resolution: 3.1→28.868 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 30.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 115.34 Å2 / Biso mean: 62.3718 Å2 / Biso min: 30 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3.1→28.868 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10
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