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- PDB-8d5j: The complex of Pre-mRNA-Processing Factor 19 (Prpf19) neoantigen ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8d5j | ||||||
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Title | The complex of Pre-mRNA-Processing Factor 19 (Prpf19) neoantigen KYLQVASHV Presented by H2-Kd | ||||||
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![]() | IMMUNE SYSTEM / Complex / MHC | ||||||
Function / homology | ![]() Formation of TC-NER Pre-Incision Complex / mRNA Splicing - Major Pathway / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / DNA replication factor A complex / positive regulation of astrocyte differentiation / Prp19 complex / U2-type catalytic step 1 spliceosome / U2-type catalytic step 2 spliceosome / Endosomal/Vacuolar pathway ...Formation of TC-NER Pre-Incision Complex / mRNA Splicing - Major Pathway / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / DNA replication factor A complex / positive regulation of astrocyte differentiation / Prp19 complex / U2-type catalytic step 1 spliceosome / U2-type catalytic step 2 spliceosome / Endosomal/Vacuolar pathway / DAP12 interactions / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / positive regulation of mRNA splicing, via spliceosome / ER-Phagosome pathway / DAP12 signaling / ubiquitin-ubiquitin ligase activity / lipid biosynthetic process / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / spliceosomal complex assembly / protein K63-linked ubiquitination / spliceosomal tri-snRNP complex assembly / proteasomal protein catabolic process / cellular defense response / positive regulation of neuron differentiation / Neutrophil degranulation / catalytic step 2 spliceosome / lipid droplet / DNA damage checkpoint signaling / spliceosomal complex / cellular response to iron(III) ion / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / negative regulation of forebrain neuron differentiation / RING-type E3 ubiquitin transferase / regulation of erythrocyte differentiation / peptide antigen assembly with MHC class I protein complex / regulation of iron ion transport / response to molecule of bacterial origin / MHC class I peptide loading complex / HFE-transferrin receptor complex / T cell mediated cytotoxicity / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / MHC class I protein complex / multicellular organismal-level iron ion homeostasis / negative regulation of neurogenesis / positive regulation of receptor-mediated endocytosis / peptide antigen assembly with MHC class II protein complex / mRNA splicing, via spliceosome / MHC class II protein complex / cellular response to nicotine / double-strand break repair via nonhomologous end joining / spindle / positive regulation of T cell mediated cytotoxicity / protein polyubiquitination / phagocytic vesicle membrane / ubiquitin-protein transferase activity / positive regulation of cellular senescence / peptide antigen binding / negative regulation of epithelial cell proliferation / antigen processing and presentation of exogenous peptide antigen via MHC class II / protein localization / positive regulation of immune response / ubiquitin protein ligase activity / sensory perception of smell / positive regulation of T cell activation / negative regulation of neuron projection development / MHC class II protein complex binding / late endosome membrane / site of double-strand break / iron ion transport / T cell differentiation in thymus / protein refolding / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / membrane => GO:0016020 / learning or memory / nuclear speck / lysosomal membrane / external side of plasma membrane / structural molecule activity / Golgi apparatus / protein homodimerization activity / extracellular space / identical protein binding / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Custodio, J.M.F. / Baker, B.M. | ||||||
Funding support | ![]()
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![]() | ![]() Title: The complex of Pre-mRNA-Processing Factor 19 (Prpf19) neoantigen KYLQVASHV Presented by H2-Kd Authors: Custodio, J.M.F. / Baker, B.M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 219.9 KB | Display | ![]() |
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PDB format | ![]() | 134.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 438.8 KB | Display | ![]() |
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Full document | ![]() | 441.6 KB | Display | |
Data in XML | ![]() | 16.8 KB | Display | |
Data in CIF | ![]() | 23.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1vgkS S: Starting model for refinement |
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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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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 32245.816 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Protein | Mass: 11835.555 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
#3: Protein/peptide | Mass: 1046.219 Da / Num. of mol.: 1 / Fragment: UNP residues 206-214 / Source method: obtained synthetically / Source: (synth.) ![]() ![]() References: UniProt: Q99KP6, RING-type E3 ubiquitin transferase |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.4336634 Å3/Da / Density % sol: 49.490311 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 20% w/v PEG3000, 100 mM HEPES, 200 mM sodium acetate |
-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: Nov 23, 2020 | |||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 | |||||||||||||||||||||
Reflection | Resolution: 1.95→40.902 Å / Num. obs: 30593 / % possible obs: 97.1 % / Redundancy: 4.7 % / CC1/2: 0.991 / Rmerge(I) obs: 0.138 / Rpim(I) all: 0.103 / Rrim(I) all: 0.173 / Net I/σ(I): 15.9 | |||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 1VGK Resolution: 1.95→40.902 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.943 / WRfactor Rfree: 0.246 / WRfactor Rwork: 0.201 / SU B: 8.752 / SU ML: 0.117 / Average fsc free: 0.9598 / Average fsc work: 0.9734 / Cross valid method: THROUGHOUT / ESU R: 0.169 / ESU R Free: 0.155 / Details: Hydrogens have not been used
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 39.061 Å2
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Refinement step | Cycle: LAST / Resolution: 1.95→40.902 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
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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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