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Yorodumi- PDB-4j8r: Structure of an octapeptide repeat of the prion protein bound to ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4j8r | ||||||
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Title | Structure of an octapeptide repeat of the prion protein bound to the POM2 Fab antibody fragment | ||||||
Components |
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Keywords | IMMUNE SYSTEM / Immunoglobulin fold / Fab / Antibody / Octapeptide repeat / Mouse prion protein | ||||||
Function / homology | Function and homology information Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / 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 / negative regulation of dendritic spine maintenance / glycosaminoglycan binding / ATP-dependent protein binding / negative regulation of interleukin-17 production ...Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / 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 / negative regulation of dendritic spine maintenance / glycosaminoglycan binding / ATP-dependent protein binding / negative regulation of interleukin-17 production / type 5 metabotropic glutamate receptor binding / cupric ion binding / regulation of potassium ion transmembrane transport / nucleobase-containing compound metabolic process / response to copper ion / negative regulation of calcineurin-NFAT signaling cascade / negative regulation of T cell receptor signaling pathway / negative regulation of interleukin-2 production / activation of protein kinase activity / negative regulation of amyloid-beta formation / negative regulation of activated T cell proliferation / cuprous ion binding / response to amyloid-beta / negative regulation of type II interferon production / negative regulation of long-term synaptic potentiation / intracellular copper ion homeostasis / positive regulation of protein targeting to membrane / response to cadmium ion / side of membrane / regulation of peptidyl-tyrosine phosphorylation / inclusion body / cellular response to copper ion / neuron projection maintenance / positive regulation of calcium-mediated signaling / negative regulation of protein phosphorylation / molecular function activator activity / positive regulation of protein localization to plasma membrane / molecular condensate scaffold activity / protein destabilization / negative regulation of DNA-binding transcription factor activity / protein homooligomerization / terminal bouton / positive regulation of neuron apoptotic process / cellular response to amyloid-beta / positive regulation of peptidyl-tyrosine phosphorylation / cellular response to xenobiotic stimulus / regulation of protein localization / protein-folding chaperone binding / signaling receptor activity / amyloid-beta binding / microtubule binding / protease binding / nuclear membrane / transmembrane transporter binding / response to oxidative stress / molecular adaptor activity / postsynaptic density / learning or memory / membrane raft / copper ion binding / dendrite / protein-containing complex binding / negative regulation of apoptotic process / Golgi apparatus / cell surface / endoplasmic reticulum / identical protein binding / membrane / metal ion binding / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.303 Å | ||||||
Authors | Swayampakula, M. / Baral, P.K. / Kav, N.N.V. / Aguzzi, A. / James, M.N.G. | ||||||
Citation | Journal: Protein Sci. / Year: 2013 Title: The crystal structure of an octapeptide repeat of the Prion protein in complex with a Fab fragment of the POM2 antibody. Authors: Swayampakula, M. / Baral, P.K. / Aguzzi, A. / Kav, N.N. / James, M.N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4j8r.cif.gz | 332.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4j8r.ent.gz | 275.2 KB | Display | PDB format |
PDBx/mmJSON format | 4j8r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4j8r_validation.pdf.gz | 478.8 KB | Display | wwPDB validaton report |
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Full document | 4j8r_full_validation.pdf.gz | 511.4 KB | Display | |
Data in XML | 4j8r_validation.xml.gz | 37.3 KB | Display | |
Data in CIF | 4j8r_validation.cif.gz | 51.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j8/4j8r ftp://data.pdbj.org/pub/pdb/validation_reports/j8/4j8r | HTTPS FTP |
-Related structure data
Related structure data | 4dgiS 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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2 |
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Unit cell |
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-Components
#1: Antibody | Mass: 23133.510 Da / Num. of mol.: 2 / Fragment: unp residues 67-82 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) #2: Antibody | Mass: 23188.998 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) #3: Protein/peptide | Mass: 1633.682 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Mus musculus (house mouse) / References: UniProt: P04925 #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.53 Å3/Da / Density % sol: 51.44 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 28% PEG 1000, 0.1M HEPES, 0.2M Calcium Chloride, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.979 Å |
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: May 28, 2011 |
Radiation | Monochromator: Double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→39.6 Å / Num. all: 44155 / Num. obs: 44080 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.24 % / Biso Wilson estimate: 47.98 Å2 / Net I/σ(I): 10.82 |
Reflection shell | Resolution: 2.3→2.35 Å / % possible all: 98 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4DGI Resolution: 2.303→39.597 Å / SU ML: 0.33 / σ(F): 1.34 / Phase error: 27.31 / Stereochemistry target values: ML Details: The Rmeas for the data collection is 0.161 (overall data)
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.39 Å / Luzzati d res low obs: 2.3 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.303→39.597 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 11.0193 Å / Origin y: -13.508 Å / Origin z: 27.3858 Å
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Refinement TLS group | Selection details: all |