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Yorodumi- PDB-8d5k: The complex of Pre-mRNA-Processing Factor 19 (Prpf19) peptide KYL... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8d5k | ||||||
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Title | The complex of Pre-mRNA-Processing Factor 19 (Prpf19) peptide KYLQVASHV Presented by H2-Kd | ||||||
Components |
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Keywords | IMMUNE SYSTEM / Complex / MHC | ||||||
Function / homology | Function and homology information 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 / antigen processing and presentation of exogenous peptide antigen via MHC class I / inner ear development / protein K63-linked ubiquitination / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / spliceosomal tri-snRNP complex assembly / proteasomal protein catabolic process / beta-2-microglobulin binding / cellular defense response / positive regulation of neuron differentiation / Neutrophil degranulation / catalytic step 2 spliceosome / lipid droplet / peptide binding / DNA damage checkpoint signaling / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / lumenal side of endoplasmic reticulum membrane / 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 / spindle / double-strand break repair via nonhomologous end joining / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / protein polyubiquitination / phagocytic vesicle membrane / ubiquitin-protein transferase activity / peptide antigen binding / positive regulation of cellular senescence / negative regulation of epithelial cell proliferation / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / ubiquitin protein ligase activity / positive regulation of T cell activation / protein localization / sensory perception of smell / 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 / learning or memory / nuclear speck / defense response to bacterium / immune response / external side of plasma membrane / lysosomal membrane / signaling receptor binding / protein-containing complex binding / structural molecule activity / Golgi apparatus / protein homodimerization activity / extracellular space / identical protein binding / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.066 Å | ||||||
Authors | Custodio, J.M.F. / Baker, B.M. | ||||||
Funding support | United States, 1items
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Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2023 Title: Structural and physical features that distinguish tumor-controlling from inactive cancer neoepitopes. Authors: Custodio, J.M. / Ayres, C.M. / Rosales, T.J. / Brambley, C.A. / Arbuiso, A.G. / Landau, L.M. / Keller, G.L.J. / Srivastava, P.K. / Baker, B.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8d5k.cif.gz | 218 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8d5k.ent.gz | 134.6 KB | Display | PDB format |
PDBx/mmJSON format | 8d5k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8d5k_validation.pdf.gz | 443.2 KB | Display | wwPDB validaton report |
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Full document | 8d5k_full_validation.pdf.gz | 446.5 KB | Display | |
Data in XML | 8d5k_validation.xml.gz | 16.2 KB | Display | |
Data in CIF | 8d5k_validation.cif.gz | 21.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d5/8d5k ftp://data.pdbj.org/pub/pdb/validation_reports/d5/8d5k | HTTPS FTP |
-Related structure data
Related structure data | 8d5eC 8d5fC 1vgkS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 32114.625 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: H2-K1, H2-K / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P01902 |
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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.) Mus musculus (house mouse) / Gene: B2m / Plasmid: pGMT7 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P01887 |
#3: Protein/peptide | Mass: 1090.255 Da / Num. of mol.: 1 / Fragment: UNP residues 206-214 / Source method: obtained synthetically / Source: (synth.) Mus musculus (house mouse) References: UniProt: Q99KP6, RING-type E3 ubiquitin transferase |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.4348 Å3/Da / Density % sol: 49.5142 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, hanging drop / Details: 10% w/v PEG8000, 200 mM magnesium acetate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-E / Wavelength: 0.98 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 10, 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→41.349 Å / Num. obs: 23784 / % possible obs: 90.4 % / Redundancy: 2.3 % / CC1/2: 0.993 / Rmerge(I) obs: 0.069 / Rpim(I) all: 0.067 / Rrim(I) all: 0.096 / Net I/σ(I): 14.6 |
Reflection shell | Resolution: 1.95→2 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.281 / Num. unique obs: 8577 / CC1/2: 0.899 / Rpim(I) all: 0.278 / Rrim(I) all: 0.396 / % possible all: 97 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1VGK Resolution: 2.066→41.349 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.948 / SU B: 11.527 / SU ML: 0.146 / Cross valid method: THROUGHOUT / ESU R: 0.253 / ESU R Free: 0.191 / 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: 46.908 Å2
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Refinement step | Cycle: LAST / Resolution: 2.066→41.349 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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