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Yorodumi- PDB-2x4n: Crystal structure of MHC CLass I HLA-A2.1 bound to residual fragm... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2x4n | |||||||||
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Title | Crystal structure of MHC CLass I HLA-A2.1 bound to residual fragments of a photocleavable peptide that is cleaved upon UV-light treatment | |||||||||
Components |
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Keywords | IMMUNE SYSTEM / GLYCOPROTEIN / TRANSMEMBRANE / DISEASE MUTATION / IMMUNOGLOBULIN DOMAIN / PHOSPHOPROTEIN / IMMUNE RESPONSE / HOST-VIRUS INTERACTION / PYRROLIDONE CARBOXYLIC ACID / GLYCATION / AMYLOIDOSIS | |||||||||
Function / homology | Function and homology information T cell mediated cytotoxicity directed against tumor cell target / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / positive regulation of memory T cell activation / TAP complex binding / antigen processing and presentation of exogenous peptide antigen via MHC class I / Golgi medial cisterna / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / positive regulation of CD8-positive, alpha-beta T cell proliferation / CD8 receptor binding ...T cell mediated cytotoxicity directed against tumor cell target / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / positive regulation of memory T cell activation / TAP complex binding / antigen processing and presentation of exogenous peptide antigen via MHC class I / Golgi medial cisterna / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / positive regulation of CD8-positive, alpha-beta T cell proliferation / CD8 receptor binding / endoplasmic reticulum exit site / beta-2-microglobulin binding / TAP binding / protection from natural killer cell mediated cytotoxicity / 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 / detection of bacterium / T cell receptor binding / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / early endosome lumen / positive regulation of receptor binding / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / negative regulation of receptor binding / lumenal side of endoplasmic reticulum membrane / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / cellular response to iron(III) ion / negative regulation of forebrain neuron differentiation / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / response to molecule of bacterial origin / regulation of erythrocyte differentiation / regulation of iron ion transport / MHC class I peptide loading complex / HFE-transferrin receptor complex / T cell mediated cytotoxicity / cellular response to iron ion / 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 / positive regulation of T cell mediated cytotoxicity / peptide antigen assembly with MHC class II protein complex / negative regulation of neurogenesis / MHC class II protein complex / positive regulation of receptor-mediated endocytosis / cellular response to nicotine / recycling endosome membrane / phagocytic vesicle membrane / specific granule lumen / peptide antigen binding / positive regulation of cellular senescence / antigen processing and presentation of exogenous peptide antigen via MHC class II / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon gamma signaling / positive regulation of immune response / negative regulation of epithelial cell proliferation / Modulation by Mtb of host immune system / positive regulation of T cell activation / Interferon alpha/beta signaling / positive regulation of type II interferon production / sensory perception of smell / negative regulation of neuron projection development / E3 ubiquitin ligases ubiquitinate target proteins / tertiary granule lumen / DAP12 signaling / MHC class II protein complex binding / late endosome membrane / T cell differentiation in thymus / positive regulation of protein binding / ER-Phagosome pathway / antibacterial humoral response / iron ion transport / T cell receptor signaling pathway / protein refolding / early endosome membrane / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / learning or memory / defense response to Gram-positive bacterium / immune response / Amyloid fiber formation / lysosomal membrane / endoplasmic reticulum lumen / external side of plasma membrane / Golgi membrane / signaling receptor binding / focal adhesion / innate immune response / Neutrophil degranulation / endoplasmic reticulum membrane / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / Golgi apparatus / cell surface / endoplasmic reticulum Similarity search - Function | |||||||||
Biological species | HOMO SAPIENS (human) INFLUENZA A VIRUS | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.34 Å | |||||||||
Authors | Celie, P.H.N. / Toebes, M. / Rodenko, B. / Ovaa, H. / Perrakis, A. / Schumacher, T.N.M. | |||||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 2009 Title: Uv-Induced Ligand Exchange in Mhc Class I Protein Crystals. Authors: Celie, P.H.N. / Toebes, M. / Rodenko, B. / Ovaa, H. / Perrakis, A. / Schumacher, T.N.M. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2x4n.cif.gz | 336.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2x4n.ent.gz | 275.1 KB | Display | PDB format |
PDBx/mmJSON format | 2x4n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x4/2x4n ftp://data.pdbj.org/pub/pdb/validation_reports/x4/2x4n | HTTPS FTP |
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-Related structure data
Related structure data | 2x4oC 2x4rC 2x4sC 2x4uC 2x70C 1eeyS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
-Protein , 2 types, 4 molecules ADBE
#1: Protein | Mass: 31854.203 Da / Num. of mol.: 2 / Fragment: RESIDUES 25-299 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P01892, UniProt: P04439*PLUS #2: Protein | Mass: 11879.356 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): XLI BLUE / References: UniProt: P61769 |
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-Protein/peptide , 1 types, 2 molecules CF
#3: Protein/peptide | Mass: 1146.314 Da / Num. of mol.: 2 / Source method: obtained synthetically Details: MODIFIED AT P5 (RESIDUE62) AND P8 (RESIDUE 65).(2-NITRO)PHENYL-PROPIONIC ACID AT P5 AND 3-AMINO-3-(2- NITRO)PHENYL-PROPIONIC ACID AT P8. CRYSTAL WAS EXPOSED TO UV LIGHT TO CLEAVE PEPTIDE AT ...Details: MODIFIED AT P5 (RESIDUE62) AND P8 (RESIDUE 65).(2-NITRO)PHENYL-PROPIONIC ACID AT P5 AND 3-AMINO-3-(2- NITRO)PHENYL-PROPIONIC ACID AT P8. CRYSTAL WAS EXPOSED TO UV LIGHT TO CLEAVE PEPTIDE AT PRV AND PRQ RESIDUES, RESULTING IN REMOVAL OF RESIDUES 62-64 FROM THE STRUCTURE. Source: (synth.) INFLUENZA A VIRUS |
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-Non-polymers , 3 types, 247 molecules
#4: Chemical | ChemComp-GOL / #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Details
Sequence details | INITIALIZING METHIONINE (B0 AND E0) ADDED TO SEQUENCE. ORIGINAL SEQUENCE IS GILGFVFTL. G AT P1 IS ...INITIALIZI |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 49 % / Description: NONE |
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Crystal grow | pH: 6.5 Details: 100 MM MES PH 5.5, 20% PEG 1500. CRYSTALS WERE FROZEN IN 100 MM MES, 30% PEG 1500, 10% GLYCEROL |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.0723 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Sep 6, 2007 / Details: MIRRORS |
Radiation | Monochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0723 Å / Relative weight: 1 |
Reflection | Resolution: 2.34→80.06 Å / Num. obs: 33198 / % possible obs: 92.4 % / Observed criterion σ(I): -3.7 / Redundancy: 1.88 % / Biso Wilson estimate: 43.7 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 9.02 |
Reflection shell | Resolution: 2.34→2.47 Å / Redundancy: 1.82 % / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 2.47 / % possible all: 92.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1EEY Resolution: 2.34→19.806 Å / SU ML: 0.42 / σ(F): 1.37 / Phase error: 28.79 / Stereochemistry target values: ML Details: THIS ENTRY IS RELATED TO PDB ENTRY 2X4M WHERE THE PHOTOCLEAVABLE MOIETIES PRQ AND PRV ARE DESCRBED (PRQ WA FIRST DESCRIBED IN 2VE6)
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.527 Å2 / ksol: 0.338 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 50.18 Å2
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Refinement step | Cycle: LAST / Resolution: 2.34→19.806 Å
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Refine LS restraints |
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LS refinement shell |
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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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