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Yorodumi- PDB-1xr9: Crystal Structures of HLA-B*1501 in Complex with Peptides from Hu... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1xr9 | ||||||
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Title | Crystal Structures of HLA-B*1501 in Complex with Peptides from Human UbcH6 and Epstein-Barr Virus EBNA-3 | ||||||
Components |
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Keywords | IMMUNE SYSTEM/Ligase / major histocompatibility antigen / MHC / HLA / HLA-B62 / HLA-B*1501 / complex (antigen-peptide) / IMMUNE SYSTEM-Ligase COMPLEX | ||||||
Function / homology | Function and homology information ISG15 transferase activity / ISG15-protein conjugation / Conversion from APC/C:Cdc20 to APC/C:Cdh1 in late anaphase / Inactivation of APC/C via direct inhibition of the APC/C complex / APC/C:Cdc20 mediated degradation of mitotic proteins / Aberrant regulation of mitotic exit in cancer due to RB1 defects / (E3-independent) E2 ubiquitin-conjugating enzyme / Phosphorylation of the APC/C / regulation of interleukin-12 production / regulation of dendritic cell differentiation ...ISG15 transferase activity / ISG15-protein conjugation / Conversion from APC/C:Cdc20 to APC/C:Cdh1 in late anaphase / Inactivation of APC/C via direct inhibition of the APC/C complex / APC/C:Cdc20 mediated degradation of mitotic proteins / Aberrant regulation of mitotic exit in cancer due to RB1 defects / (E3-independent) E2 ubiquitin-conjugating enzyme / Phosphorylation of the APC/C / regulation of interleukin-12 production / regulation of dendritic cell differentiation / regulation of T cell anergy / regulation of interleukin-6 production / E2 ubiquitin-conjugating enzyme / ubiquitin conjugating enzyme activity / Regulation of APC/C activators between G1/S and early anaphase / Transcriptional Regulation by VENTX / protein K48-linked ubiquitination / ubiquitin ligase complex / 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 / APC/C:Cdc20 mediated degradation of Cyclin B / APC-Cdc20 mediated degradation of Nek2A / detection of bacterium / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / secretory granule membrane / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / Autodegradation of Cdh1 by Cdh1:APC/C / early endosome lumen / positive regulation of receptor binding / APC/C:Cdc20 mediated degradation of Securin / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / negative regulation of receptor binding / Assembly of the pre-replicative complex / lumenal side of endoplasmic reticulum membrane / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / 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 / defense response / 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 / ISG15 antiviral mechanism / cellular response to iron ion / CDK-mediated phosphorylation and removal of Cdc6 / 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 / protein polyubiquitination / MHC class II protein complex / positive regulation of receptor-mediated endocytosis / cellular response to nicotine / recycling endosome membrane / ubiquitin-protein transferase activity / phagocytic vesicle membrane / specific granule lumen / peptide antigen binding / Separation of Sister Chromatids / 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 / sensory perception of smell / Antigen processing: Ubiquitination & Proteasome degradation / 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 / iron ion transport / ubiquitin-dependent protein catabolic process / protein-folding chaperone binding / Senescence-Associated Secretory Phenotype (SASP) / protein refolding / early endosome membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.788 Å | ||||||
Authors | Roder, G. / Blicher, T. / Johannessen, B.R. / Kristensen, O. / Buus, S. / Gajhede, M. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2006 Title: Crystal structures of two peptide-HLA-B*1501 complexes; structural characterization of the HLA-B62 supertype Authors: Roder, G. / Blicher, T. / Justesen, S. / Johannesen, B. / Kristensen, O. / Kastrup, J. / Buus, S. / Gajhede, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1xr9.cif.gz | 110.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1xr9.ent.gz | 83.4 KB | Display | PDB format |
PDBx/mmJSON format | 1xr9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xr/1xr9 ftp://data.pdbj.org/pub/pdb/validation_reports/xr/1xr9 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 31958.195 Da / Num. of mol.: 1 / Fragment: residues 1-276 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-Bw62.1 / Plasmid: pET28a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P30464, UniProt: P01889*PLUS |
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#2: Protein | Mass: 11748.160 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: B2M / Plasmid: pET28a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P61769 |
-Protein/peptide , 1 types, 1 molecules C
#3: Protein/peptide | Mass: 902.046 Da / Num. of mol.: 1 / Fragment: residues 83-91 / Source method: obtained synthetically / Details: CHEMICAL SYNTHESIS / References: UniProt: P51965, ubiquitin-protein ligase |
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-Non-polymers , 4 types, 599 molecules
#4: Chemical | #5: Chemical | ChemComp-URE / | #6: Chemical | ChemComp-GOL / | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 50 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 0.2M NH4Ac, 0.1M tri-Sodium Citrate dihydrate, pH 5.6, 30% w/v PEG4000, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.8414 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jul 20, 2004 |
Radiation | Monochromator: Bent Single-Crystal Germanium Triangular Monochromator Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8414 Å / Relative weight: 1 |
Reflection | Resolution: 1.776→31.654 Å / Num. obs: 43204 / % possible obs: 97.44 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 17.4 Å2 / Rsym value: 0.068 / Net I/σ(I): 14.2 |
Reflection shell | Resolution: 1.78→1.87 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 2.5 / Num. measured all: 19646 / Num. unique all: 19646 / Rsym value: 0.298 / % possible all: 83.32 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: B*1501/LEKARGSTY Complex without Peptide Resolution: 1.788→19.083 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.926 / WRfactor Rfree: 0.224 / WRfactor Rwork: 0.172 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Solvent model: MASK BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.306 Å2
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Refinement step | Cycle: LAST / Resolution: 1.788→19.083 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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