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Yorodumi- PDB-3rew: Crystal structure of an lmp2a-derived peptide bound to human clas... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3rew | ||||||
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Title | Crystal structure of an lmp2a-derived peptide bound to human class i mhc hla-a2 | ||||||
Components |
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Keywords | IMMUNE SYSTEM / MHC CLASS I / TUMOUR ANTIGEN TARGETING / HLA-A2 / EPSTEIN BARR VIRUS / ALLOREACTIVITY / GLYCOPROTEIN / IMMUNE RESPONSE / MHC I / IMMUNOGLOBULIN DOMAIN | ||||||
Function / homology | Function and homology information host cell endomembrane system / viral latency / T cell mediated cytotoxicity directed against tumor cell target / positive regulation of memory T cell activation / TAP complex binding / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / Golgi medial cisterna / positive regulation of CD8-positive, alpha-beta T cell proliferation / CD8 receptor binding ...host cell endomembrane system / viral latency / T cell mediated cytotoxicity directed against tumor cell target / positive regulation of memory T cell activation / TAP complex binding / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / Golgi medial cisterna / positive regulation of CD8-positive, alpha-beta T cell proliferation / CD8 receptor binding / antigen processing and presentation of exogenous peptide antigen via MHC class I / endoplasmic reticulum exit site / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / TAP binding / protection from natural killer cell mediated cytotoxicity / beta-2-microglobulin binding / T cell receptor binding / detection of bacterium / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / negative regulation of receptor binding / 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 / cellular response to iron ion / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / 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 / regulation of erythrocyte differentiation / ER to Golgi transport vesicle membrane / 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 / peptide antigen assembly with MHC class II protein complex / positive regulation of receptor-mediated endocytosis / MHC class II protein complex / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / specific granule lumen / recycling endosome membrane / phagocytic vesicle membrane / peptide antigen binding / positive regulation of cellular senescence / antigen processing and presentation of exogenous peptide antigen via MHC class II / negative regulation of epithelial cell proliferation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon gamma signaling / positive regulation of immune response / Modulation by Mtb of host immune system / positive regulation of type II interferon production / Interferon alpha/beta signaling / sensory perception of smell / positive regulation of T cell activation / positive regulation of protein binding / tertiary granule lumen / E3 ubiquitin ligases ubiquitinate target proteins / DAP12 signaling / negative regulation of neuron projection development / MHC class II protein complex binding / late endosome membrane / T cell receptor signaling pathway / ER-Phagosome pathway / iron ion transport / early endosome membrane / antibacterial humoral response / T cell differentiation in thymus / protein refolding / symbiont-mediated perturbation of host ubiquitin-like protein modification / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / learning or memory / host cell perinuclear region of cytoplasm / defense response to Gram-positive bacterium / immune response / Amyloid fiber formation / endoplasmic reticulum lumen / lysosomal membrane / external side of plasma membrane / Golgi membrane / innate immune response / focal adhesion / signaling receptor binding / Neutrophil degranulation / endoplasmic reticulum membrane / SARS-CoV-2 activates/modulates innate and adaptive immune responses Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Human herpesvirus 4 (Epstein-Barr virus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Wood, A. / Mohammed, F. / Salim, M. / Tranter, A. / Rickinson, A.B. / Moss, P.A.H. / Stauss, H.J. / Steven, N.M. / Willcox, B.E. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2011 Title: Structural and energetic evidence for highly peptide-specific tumor antigen targeting via allo-MHC restriction. Authors: Simpson, A.A. / Mohammed, F. / Salim, M. / Tranter, A. / Rickinson, A.B. / Stauss, H.J. / Moss, P.A. / Steven, N.M. / Willcox, B.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3rew.cif.gz | 176.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3rew.ent.gz | 138.7 KB | Display | PDB format |
PDBx/mmJSON format | 3rew.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3rew_validation.pdf.gz | 479.8 KB | Display | wwPDB validaton report |
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Full document | 3rew_full_validation.pdf.gz | 488.3 KB | Display | |
Data in XML | 3rew_validation.xml.gz | 33.7 KB | Display | |
Data in CIF | 3rew_validation.cif.gz | 48.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/re/3rew ftp://data.pdbj.org/pub/pdb/validation_reports/re/3rew | HTTPS FTP |
-Related structure data
Related structure data | 3revC 1bd2S 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 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-A, HLAA / Plasmid: PGMT7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)PLYSS / References: UniProt: P01892, UniProt: P04439*PLUS #2: Protein | Mass: 11748.160 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Plasmid: PGMT7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)PLYSS / References: UniProt: P61769 |
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-Protein/peptide , 1 types, 2 molecules CF
#3: Protein/peptide | Mass: 906.165 Da / Num. of mol.: 2 / Fragment: LATENT MEMBRANE PROTEIN 2 (unp residues 426-434) / Source method: obtained synthetically Details: THE PEPTIDE WAS CHEMICALLY SYNTHESIZED. COMMERCIAL SYNTHESIS. Source: (synth.) Human herpesvirus 4 (strain B95-8) (Epstein-Barr virus (strain B95-8)) References: UniProt: P13285 |
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-Non-polymers , 4 types, 455 molecules
#4: Chemical | ChemComp-IOD / #5: Chemical | #6: Chemical | ChemComp-CL / #7: Water | ChemComp-HOH / | |
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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: 2.8 Å3/Da / Density % sol: 56.07 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop Details: 22% PEG 3350, 0.2M AMMONIUM IODIDE, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.979355 |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 29, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979355 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→100 Å / Num. obs: 79598 / % possible obs: 99.8 % / Redundancy: 4.4 % / Rmerge(I) obs: 0.095 / Net I/σ(I): 5.803 |
Reflection shell | Resolution: 1.9→2 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.485 / Mean I/σ(I) obs: 1.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 1BD2 Resolution: 1.9→39.11 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.916 / SU B: 2.984 / SU ML: 0.091 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.136 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.06 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→39.11 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.95 Å / Total num. of bins used: 20
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