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Yorodumi- PDB-3hae: Rational development of high-affinity T-cell receptor-like antibodies -
+Open data
-Basic information
Entry | Database: PDB / ID: 3hae | |||||||||
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Title | Rational development of high-affinity T-cell receptor-like antibodies | |||||||||
Components |
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Keywords | IMMUNE SYSTEM / Fab / Major Histocompatability Complex / Immunity / Disulfide bond / Glycoprotein / Host-virus interaction / Immune response / Membrane / MHC I / Phosphoprotein / Transmembrane / Disease mutation / Glycation / Immunoglobulin domain / Pyrrolidone carboxylic acid / Secreted | |||||||||
Function / homology | Function and homology information tRNA threonylcarbamoyladenosine metabolic process / 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 ...tRNA threonylcarbamoyladenosine metabolic process / 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 / 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 / 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 / structural molecule activity / Golgi apparatus / cell surface Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å | |||||||||
Authors | Stewart-Jones, G. / Wadle, A. / Hombach, A. / Shenderov, E. / Held, G. / Fischer, E. | |||||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2009 Title: Rational development of high-affinity T-cell receptor-like antibodies Authors: Stewart-Jones, G. / Wadle, A. / Hombach, A. / Shenderov, E. / Held, G. / Fischer, E. / Kleber, S. / Stenner-Liewen, F. / Bauer, S. / McMichael, A. / Knuth, A. / Abken, H. / Hombach, A.A. / ...Authors: Stewart-Jones, G. / Wadle, A. / Hombach, A. / Shenderov, E. / Held, G. / Fischer, E. / Kleber, S. / Stenner-Liewen, F. / Bauer, S. / McMichael, A. / Knuth, A. / Abken, H. / Hombach, A.A. / Cerundolo, V. / Jones, E.Y. / Renner, C. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3hae.cif.gz | 541.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3hae.ent.gz | 453 KB | Display | PDB format |
PDBx/mmJSON format | 3hae.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3hae_validation.pdf.gz | 581.3 KB | Display | wwPDB validaton report |
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Full document | 3hae_full_validation.pdf.gz | 683.7 KB | Display | |
Data in XML | 3hae_validation.xml.gz | 102.5 KB | Display | |
Data in CIF | 3hae_validation.cif.gz | 144.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ha/3hae ftp://data.pdbj.org/pub/pdb/validation_reports/ha/3hae | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
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-Components
#1: Protein | Mass: 31951.316 Da / Num. of mol.: 4 / Fragment: UNP residues 25-300 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: PETT22 b+ / Production host: Escherichia coli (E. coli) / References: UniProt: P01892, UniProt: P04439*PLUS #2: Protein | Mass: 11879.356 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: PETT22 b+ / Production host: Escherichia coli (E. coli) / References: UniProt: P61769 #3: Protein/peptide | Mass: 1090.335 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: This sequence occurs naturally in humans. / References: UniProt: P78358*PLUS #4: Antibody | Mass: 22740.143 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pHEN / Production host: Escherichia coli (E. coli) / Strain (production host): HB2151 #5: Antibody | Mass: 22893.605 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pHEN / Production host: Escherichia coli (E. coli) / Strain (production host): HB2151 |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.64 Å3/Da / Density % sol: 53.48 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion / pH: 6.9 Details: 12% PEG 8000, 50mM Mes, pH 6.9, VAPOR DIFFUSION, temperature 294K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.933 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: May 5, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→30 Å / Num. obs: 84609 / % possible obs: 97.8 % / Rmerge(I) obs: 0.118 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→25 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.853 / SU B: 32.96 / SU ML: 0.387 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.478 / 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: 2 Å2
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Refinement step | Cycle: LAST / Resolution: 2.9→25 Å
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Refine LS restraints |
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Refine LS restraints NCS | Refine-ID: X-RAY DIFFRACTION
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