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Yorodumi- PDB-2rfx: Crystal Structure of HLA-B*5701, presenting the self peptide, LSS... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2rfx | ||||||
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Title | Crystal Structure of HLA-B*5701, presenting the self peptide, LSSPVTKSF | ||||||
Components |
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Keywords | IMMUNE SYSTEM / alpha beta sandwich-immunologlobulin like / Glycoprotein / Host-virus interaction / Immune response / Membrane / MHC I / Transmembrane / Disease mutation / Glycation / Immunoglobulin domain / Pyrrolidone carboxylic acid / Secreted | ||||||
Function / homology | Function and homology information IgD immunoglobulin complex / IgM immunoglobulin complex / IgA immunoglobulin complex / IgE immunoglobulin complex / CD22 mediated BCR regulation / regulation of interleukin-12 production / regulation of dendritic cell differentiation / regulation of T cell anergy / IgG immunoglobulin complex / Fc epsilon receptor (FCERI) signaling ...IgD immunoglobulin complex / IgM immunoglobulin complex / IgA immunoglobulin complex / IgE immunoglobulin complex / CD22 mediated BCR regulation / regulation of interleukin-12 production / regulation of dendritic cell differentiation / regulation of T cell anergy / IgG immunoglobulin complex / Fc epsilon receptor (FCERI) signaling / regulation of interleukin-6 production / Classical antibody-mediated complement activation / Initial triggering of complement / TAP binding / FCGR activation / protection from natural killer cell mediated cytotoxicity / immunoglobulin mediated immune response / Role of phospholipids in phagocytosis / Role of LAT2/NTAL/LAB on calcium mobilization / Scavenging of heme from plasma / detection of bacterium / FCERI mediated Ca+2 mobilization / FCGR3A-mediated IL10 synthesis / secretory granule membrane / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / 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 / Regulation of Complement cascade / 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 / Cell surface interactions at the vascular wall / FCERI mediated MAPK activation / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / FCGR3A-mediated phagocytosis / antigen binding / B cell receptor signaling pathway / 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 / Regulation of actin dynamics for phagocytic cup formation / MHC class I protein complex / defense response / multicellular organismal-level iron ion homeostasis / FCERI mediated NF-kB activation / 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 / 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 / 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 / Interferon alpha/beta signaling / sensory perception of smell / positive regulation of T cell activation / positive regulation of protein binding / tertiary granule lumen / DAP12 signaling / negative regulation of neuron projection development / MHC class II protein complex binding / late endosome membrane / iron ion transport / ER-Phagosome pathway / early endosome membrane / protein-folding chaperone binding / T cell differentiation in thymus / protein refolding / protein homotetramerization / intracellular iron ion homeostasis / adaptive immune response / amyloid fibril formation / Potential therapeutics for SARS / learning or memory Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.5 Å | ||||||
Authors | Archbold, J.K. / Macdonald, W.A. / Rossjohn, J. / McCluskey, J. | ||||||
Citation | Journal: Immunity / Year: 2008 Title: Human leukocyte antigen class I-restricted activation of CD8+ T cells provides the immunogenetic basis of a systemic drug hypersensitivity Authors: Chessman, D. / Kostenko, L. / Lethborg, T. / Purcell, A.W. / Williamson, N.A. / Chen, Z. / Kjer-Nielsen, L. / Mifsud, N.A. / Tait, B.D. / Holdsworth, R. / Almeida, C.A. / Nolan, D. / ...Authors: Chessman, D. / Kostenko, L. / Lethborg, T. / Purcell, A.W. / Williamson, N.A. / Chen, Z. / Kjer-Nielsen, L. / Mifsud, N.A. / Tait, B.D. / Holdsworth, R. / Almeida, C.A. / Nolan, D. / Macdonald, W.A. / Archbold, J.K. / Kellerher, A.D. / Marriott, D. / Mallal, S. / Bharadwaj, M. / Rossjohn, J. / McCluskey, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2rfx.cif.gz | 97.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2rfx.ent.gz | 73.7 KB | Display | PDB format |
PDBx/mmJSON format | 2rfx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2rfx_validation.pdf.gz | 456.2 KB | Display | wwPDB validaton report |
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Full document | 2rfx_full_validation.pdf.gz | 461.3 KB | Display | |
Data in XML | 2rfx_validation.xml.gz | 18.6 KB | Display | |
Data in CIF | 2rfx_validation.cif.gz | 25.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rf/2rfx ftp://data.pdbj.org/pub/pdb/validation_reports/rf/2rfx | HTTPS FTP |
-Related structure data
Related structure data | 2h6pS 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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Unit cell |
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-Components
#1: Protein | Mass: 31639.059 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-B / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P18465, 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: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P61769 | ||
#3: Protein/peptide | Mass: 966.109 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: The peptide was chemically synthesized. / References: UniProt: P01834*PLUS | ||
#4: Chemical | ChemComp-GOL / #5: 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: 2.49 Å3/Da / Density % sol: 50.57 % |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-ID |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 8, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 2.5→60 Å / Num. obs: 15096 / % possible obs: 94.3 % / Redundancy: 3 % / Rmerge(I) obs: 0.081 / Net I/σ(I): 18.8 |
Reflection shell | Resolution: 2.5→2.6 Å / Redundancy: 3 % / Rmerge(I) obs: 0.312 / Mean I/σ(I) obs: 5.1 / % possible all: 89.8 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2H6P Resolution: 2.5→27.48 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.891 / SU B: 19.763 / SU ML: 0.229 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 1.794 / ESU R Free: 0.342 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 38.131 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→27.48 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.565 Å / 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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