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Open data
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Basic information
Entry | Database: PDB / ID: 6mkr | ||||||
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Title | 5287 TCR bound to IAb Padi4 | ||||||
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![]() | IMMUNE SYSTEM / T cell receptor / Major Histocompatibility Complex | ||||||
Function / homology | ![]() 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 / negative regulation of T cell proliferation / multivesicular body / post-translational protein modification / 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 / nucleosome assembly / positive regulation of T cell activation / MHC class II protein complex binding / chromatin organization / late endosome membrane / adaptive immune response / lysosome / early endosome / chromatin remodeling / immune response / lysosomal membrane / external side of plasma membrane / innate immune response / ubiquitin protein ligase binding / calcium ion binding / protein-containing complex binding / Golgi apparatus / cell surface / protein-containing complex / identical protein binding / membrane / nucleus / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Stadinski, B.D. / Blevins, S.J. / Huseby, E.S. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 278.7 KB | Display | ![]() |
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PDB format | ![]() | 223 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 449.4 KB | Display | ![]() |
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Full document | ![]() | 454.3 KB | Display | |
Data in XML | ![]() | 28.1 KB | Display | |
Data in CIF | ![]() | 38.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6mkdC ![]() 6mngC ![]() 6mnmC ![]() 6mnnC ![]() 6mnoC ![]() 4p23S C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components
#1: Protein | Mass: 20242.615 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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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.) ![]() ![]() ![]() ![]() References: UniProt: Q9Z183, UniProt: P14483, protein-arginine deiminase |
#3: Protein | Mass: 23186.578 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
#4: Protein | Mass: 26756.602 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.37 Å3/Da / Density % sol: 63.55 % / Mosaicity: 0.43 ° |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6 / Details: 14% PEG 4000, 100mM NaCacodylate, 100 mM NaCitrate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX225HE / Detector: CCD / Date: Oct 10, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97931 Å / Relative weight: 1 |
Reflection | Resolution: 3.35→128.5 Å / Num. obs: 17652 / % possible obs: 99.8 % / Redundancy: 3.6 % / Biso Wilson estimate: 68.35 Å2 / CC1/2: 0.987 / Rmerge(I) obs: 0.161 / Rpim(I) all: 0.098 / Rrim(I) all: 0.188 / Net I/σ(I): 6.7 |
Reflection shell | Resolution: 3.35→3.54 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.528 / Num. unique obs: 2542 / CC1/2: 0.904 / Rpim(I) all: 0.313 / Rrim(I) all: 0.614 / % possible all: 99.7 |
-Phasing
Phasing | Method: ![]() | |||||||||
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Phasing MR |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4P23 Resolution: 3.355→65.204 Å / SU ML: 0.47 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 29.38
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 282.07 Å2 / Biso mean: 80.9864 Å2 / Biso min: 20 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3.355→65.204 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: 6
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