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Yorodumi- PDB-3bo8: The High Resolution Crystal Structure of HLA-A1 Complexed with th... -
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-Basic information
Entry | Database: PDB / ID: 3bo8 | ||||||
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Title | The High Resolution Crystal Structure of HLA-A1 Complexed with the MAGE-A1 Peptide | ||||||
Components |
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Keywords | IMMUNE SYSTEM / Melanoma Associated Antigen / MAGE / MAGE-A1 / Major Histocompatibility Complex / MHC / Human Leukocyte Antigen / HLA / HLA-A1 / HLA-A010101 / TCR / T-cell receptor / Antibody / Fab-Hyb3 / Hyb3 / Glycoprotein / Host-virus interaction / Immune response / Immunoglobulin domain / Membrane / MHC I / Sulfation / Transmembrane / Disease mutation / Glycation / Pyrrolidone carboxylic acid / Secreted / Tumor antigen | ||||||
Function / homology | Function and homology information 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 / negative regulation of Notch signaling pathway / antigen processing and presentation of exogenous peptide antigen via MHC class I ...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 / negative regulation of Notch signaling pathway / 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 / histone deacetylase binding / 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 / positive regulation of type II interferon production / 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 / iron ion transport / ER-Phagosome pathway / early endosome membrane / antibacterial humoral response / T cell differentiation in thymus / protein refolding / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / learning or memory / defense response to Gram-positive bacterium / immune response / Amyloid fiber formation / endoplasmic reticulum lumen / Golgi membrane / lysosomal membrane / external side of plasma membrane / innate immune response / focal adhesion / signaling receptor binding / Neutrophil degranulation / endoplasmic reticulum membrane / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / Golgi apparatus Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å | ||||||
Authors | Kumar, P. / Vahedi-Faridi, A. / Saenger, W. / Ziegler, A. / Uchanska-Ziegler, B. | ||||||
Citation | Journal: Protein Sci. / Year: 2009 Title: Conformational changes within the HLA-A1:MAGE-A1 complex induced by binding of a recombinant antibody fragment with TCR-like specificity Authors: Kumar, P. / Vahedi-Faridi, A. / Saenger, W. / Ziegler, A. / Uchanska-Ziegler, B. #1: Journal: J.Biol.Chem. / Year: 2005 Title: A major histocompatibility complex-peptide-restricted antibody and t cell receptor molecules recognize their target by distinct binding modes: crystal structure of human leukocyte antigen (HLA) ...Title: A major histocompatibility complex-peptide-restricted antibody and t cell receptor molecules recognize their target by distinct binding modes: crystal structure of human leukocyte antigen (HLA)-A1-MAGE-A1 in complex with FAB-HYB3 Authors: Hulsmeyer, M. / Chames, P. / Hillig, R.C. / Stanfield, R.L. / Held, G. / Coulie, P.G. / Alings, C. / Wille, G. / Saenger, W. / Uchanska-Ziegler, B. / Hoogenboom, H.R. / Ziegler, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3bo8.cif.gz | 109 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3bo8.ent.gz | 81.1 KB | Display | PDB format |
PDBx/mmJSON format | 3bo8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3bo8_validation.pdf.gz | 458.4 KB | Display | wwPDB validaton report |
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Full document | 3bo8_full_validation.pdf.gz | 463.5 KB | Display | |
Data in XML | 3bo8_validation.xml.gz | 23.7 KB | Display | |
Data in CIF | 3bo8_validation.cif.gz | 36 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bo/3bo8 ftp://data.pdbj.org/pub/pdb/validation_reports/bo/3bo8 | HTTPS FTP |
-Related structure data
Related structure data | 1w72S 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: 31636.955 Da / Num. of mol.: 1 Fragment: Ectodomain, Alpha-1, Alpha-2, Alpha-3, UNP Residues 25-298 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3 / References: UniProt: P30443, UniProt: P04439*PLUS | ||
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#2: Protein | Mass: 11879.356 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / Strain (production host): XA90 / References: UniProt: P61769 | ||
#3: Protein/peptide | Mass: 976.964 Da / Num. of mol.: 1 / Fragment: UNP Residues 161-169 / Source method: obtained synthetically Details: solid phase synthesis; This sequence occurs naturally in humans. References: UniProt: P43355 | ||
#4: Chemical | #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: 2.68 Å3/Da / Density % sol: 54.14 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 20% PEG 3350, 0.2M Sodium Fluoride, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.954 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: May 20, 2005 / Details: mirror |
Radiation | Monochromator: Si-111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.954 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→63.888 Å / Num. obs: 43828 / % possible obs: 97 % / Redundancy: 4.1 % / Biso Wilson estimate: 18.248 Å2 / Rmerge(I) obs: 0.109 / Rsym value: 0.109 / Net I/σ(I): 17.3 |
Reflection shell | Resolution: 1.8→1.9 Å / Redundancy: 4 % / Rmerge(I) obs: 0.351 / Mean I/σ(I) obs: 3.82 / Num. measured all: 24361 / Num. unique all: 6163 / Rsym value: 0.351 / % possible all: 95 |
-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Rfactor: 0.431 / Cor.coef. Fo:Fc: 0.528
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1W72 Resolution: 1.8→19.65 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.923 / SU B: 2.672 / SU ML: 0.084 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.136 / ESU R Free: 0.125 / 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: 19.157 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→19.65 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.847 Å / Total num. of bins used: 20
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