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Yorodumi- PDB-2w9e: Structure of ICSM 18 (anti-Prp therapeutic antibody) Fab fragment... -
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-Basic information
Entry | Database: PDB / ID: 2w9e | ||||||
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Title | Structure of ICSM 18 (anti-Prp therapeutic antibody) Fab fragment complexed with human Prp fragment 119-231 | ||||||
Components |
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Keywords | IMMUNE SYSTEM / FAB / PRP / PRION / MEMBRANE / GPI-ANCHOR / LIPOPROTEIN / GOLGI APPARATUS / DISEASE MUTATION / GLYCOPROTEIN / CELL MEMBRANE | ||||||
Function / homology | Function and homology information positive regulation of glutamate receptor signaling pathway / negative regulation of amyloid precursor protein catabolic process / lamin binding / regulation of glutamate receptor signaling pathway / regulation of calcium ion import across plasma membrane / aspartic-type endopeptidase inhibitor activity / glycosaminoglycan binding / ATP-dependent protein binding / regulation of potassium ion transmembrane transport / NCAM1 interactions ...positive regulation of glutamate receptor signaling pathway / negative regulation of amyloid precursor protein catabolic process / lamin binding / regulation of glutamate receptor signaling pathway / regulation of calcium ion import across plasma membrane / aspartic-type endopeptidase inhibitor activity / glycosaminoglycan binding / ATP-dependent protein binding / regulation of potassium ion transmembrane transport / NCAM1 interactions / negative regulation of interleukin-17 production / negative regulation of dendritic spine maintenance / type 5 metabotropic glutamate receptor binding / cupric ion binding / negative regulation of protein processing / negative regulation of calcineurin-NFAT signaling cascade / dendritic spine maintenance / negative regulation of interleukin-2 production / negative regulation of T cell receptor signaling pathway / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / extrinsic component of membrane / cuprous ion binding / negative regulation of amyloid-beta formation / negative regulation of activated T cell proliferation / response to amyloid-beta / : / negative regulation of type II interferon production / intracellular copper ion homeostasis / negative regulation of long-term synaptic potentiation / positive regulation of protein targeting to membrane / long-term memory / response to cadmium ion / regulation of peptidyl-tyrosine phosphorylation / inclusion body / cellular response to copper ion / neuron projection maintenance / tubulin binding / negative regulation of protein phosphorylation / molecular condensate scaffold activity / molecular function activator activity / positive regulation of protein localization to plasma membrane / protein destabilization / protein homooligomerization / negative regulation of DNA-binding transcription factor activity / terminal bouton / cellular response to amyloid-beta / positive regulation of peptidyl-tyrosine phosphorylation / positive regulation of neuron apoptotic process / cellular response to xenobiotic stimulus / signaling receptor activity / amyloid-beta binding / protein-folding chaperone binding / postsynapse / microtubule binding / nuclear membrane / protease binding / response to oxidative stress / transmembrane transporter binding / postsynaptic density / molecular adaptor activity / learning or memory / regulation of cell cycle / membrane raft / copper ion binding / cell cycle / external side of plasma membrane / intracellular membrane-bounded organelle / dendrite / protein-containing complex binding / negative regulation of apoptotic process / Golgi apparatus / cell surface / endoplasmic reticulum / extracellular exosome / identical protein binding / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) MUS MUSCULUS (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å | ||||||
Authors | Antonyuk, S.V. / Trevitt, C.R. / Strange, R.W. / Jackson, G.S. / Sangar, D. / Batchelor, M. / Jones, S. / Georgiou, T. / Cooper, S. / Fraser, C. ...Antonyuk, S.V. / Trevitt, C.R. / Strange, R.W. / Jackson, G.S. / Sangar, D. / Batchelor, M. / Jones, S. / Georgiou, T. / Cooper, S. / Fraser, C. / Khalili-Shirazi, A. / Clarke, A.R. / Hasnain, S.S. / Collinge, J. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2009 Title: Crystal Structure of Human Prion Protein Bound to a Therapeutic Antibody. Authors: Antonyuk, S.V. / Trevitt, C.R. / Strange, R.W. / Jackson, G.S. / Sangar, D. / Batchelor, M. / Cooper, S. / Fraser, C. / Jones, S. / Georgiou, T. / Khalili-Shirazi, A. / Clarke, A.R. / ...Authors: Antonyuk, S.V. / Trevitt, C.R. / Strange, R.W. / Jackson, G.S. / Sangar, D. / Batchelor, M. / Cooper, S. / Fraser, C. / Jones, S. / Georgiou, T. / Khalili-Shirazi, A. / Clarke, A.R. / Hasnain, S.S. / Collinge, J. | ||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2w9e.cif.gz | 115.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2w9e.ent.gz | 89.1 KB | Display | PDB format |
PDBx/mmJSON format | 2w9e.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w9/2w9e ftp://data.pdbj.org/pub/pdb/validation_reports/w9/2w9e | HTTPS FTP |
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-Related structure data
Related structure data | 2w9dC 1uw3S S: Starting model for refinement C: citing same article (ref.) |
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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: 13231.674 Da / Num. of mol.: 1 / Fragment: RESIDUES 119-231 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P04156 |
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#2: Antibody | Mass: 23045.619 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) MUS MUSCULUS (house mouse) |
#3: Antibody | Mass: 23283.688 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) MUS MUSCULUS (house mouse) |
#4: Chemical | ChemComp-SO4 / |
#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: 2.2 Å3/Da / Density % sol: 44 % / Description: NONE |
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Crystal grow | pH: 8 / Details: AMMONIUM SULPHATE, TRIS PH 8.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX10.1 / Wavelength: 0.98 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Feb 7, 2008 / Details: MIRRORS |
Radiation | Monochromator: SI111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.85→27 Å / Num. obs: 13209 / % possible obs: 86.2 % / Redundancy: 8 % / Biso Wilson estimate: 62 Å2 / Rmerge(I) obs: 0.14 / Net I/σ(I): 12 |
Reflection shell | Resolution: 2.85→2.95 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.67 / Mean I/σ(I) obs: 2 / % possible all: 70 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1UW3 Resolution: 2.9→50 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.854 / SU B: 39.624 / SU ML: 0.357 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.447 / 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: 40.62 Å2
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Refinement step | Cycle: LAST / Resolution: 2.9→50 Å
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