+Open data
-Basic information
Entry | Database: PDB / ID: 4hmr | ||||||
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Title | Crystal structure of mutant rabbit PRP 121-230 (S170N/S174N) | ||||||
Components | Major prion protein | ||||||
Keywords | MEMBRANE PROTEIN / prp / prion / Membrane | ||||||
Function / homology | Function and homology information regulation of glutamate receptor signaling pathway / regulation of calcium ion import across plasma membrane / aspartic-type endopeptidase inhibitor activity / glycosaminoglycan binding / regulation of potassium ion transmembrane transport / negative regulation of interleukin-17 production / negative regulation of dendritic spine maintenance / type 5 metabotropic glutamate receptor binding / cupric ion binding / negative regulation of calcineurin-NFAT signaling cascade ...regulation of glutamate receptor signaling pathway / regulation of calcium ion import across plasma membrane / aspartic-type endopeptidase inhibitor activity / glycosaminoglycan binding / regulation of potassium ion transmembrane transport / negative regulation of interleukin-17 production / negative regulation of dendritic spine maintenance / type 5 metabotropic glutamate receptor binding / cupric ion binding / negative regulation of calcineurin-NFAT signaling cascade / negative regulation of T cell receptor signaling pathway / negative regulation of interleukin-2 production / cuprous ion binding / negative regulation of amyloid-beta formation / negative regulation of activated T cell proliferation / negative regulation of type II interferon production / positive regulation of protein targeting to membrane / side of membrane / inclusion body / cellular response to copper ion / neuron projection maintenance / positive regulation of protein localization to plasma membrane / molecular condensate scaffold activity / negative regulation of protein phosphorylation / molecular function activator activity / protein destabilization / protein homooligomerization / terminal bouton / cellular response to xenobiotic stimulus / cellular response to amyloid-beta / positive regulation of peptidyl-tyrosine phosphorylation / positive regulation of neuron apoptotic process / signaling receptor activity / amyloid-beta binding / nuclear membrane / microtubule binding / protease binding / response to oxidative stress / learning or memory / membrane raft / copper ion binding / dendrite / negative regulation of apoptotic process / protein-containing complex binding / cell surface / Golgi apparatus / endoplasmic reticulum / identical protein binding / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Oryctolagus cuniculus (rabbit) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Sweeting, B. / Chakrabartty, A. / Pai, E.F. | ||||||
Citation | Journal: Plos One / Year: 2013 Title: N-Terminal Helix-Cap in alpha-Helix 2 Modulates beta-State Misfolding in Rabbit and Hamster Prion Proteins. Authors: Sweeting, B. / Brown, E. / Khan, M.Q. / Chakrabartty, A. / Pai, E.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4hmr.cif.gz | 107.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4hmr.ent.gz | 82.4 KB | Display | PDB format |
PDBx/mmJSON format | 4hmr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4hmr_validation.pdf.gz | 463.4 KB | Display | wwPDB validaton report |
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Full document | 4hmr_full_validation.pdf.gz | 468.2 KB | Display | |
Data in XML | 4hmr_validation.xml.gz | 12 KB | Display | |
Data in CIF | 4hmr_validation.cif.gz | 16.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hm/4hmr ftp://data.pdbj.org/pub/pdb/validation_reports/hm/4hmr | HTTPS FTP |
-Related structure data
Related structure data | 4hlsC 4hmmC 3o79S C: citing same article (ref.) 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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3 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 15293.979 Da / Num. of mol.: 2 / Fragment: UNP residues 119-229 / Mutation: S170N, S174N Source method: isolated from a genetically manipulated source Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Gene: PRNP, PRP / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (AI) / References: UniProt: Q95211 #2: Chemical | #3: Chemical | #4: Chemical | #5: 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: 1.82 Å3/Da / Density % sol: 32.3 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 100mM SODIUM CACODYLATE PH 6.5, 3.0M NACL, 30% GLYCEROL (cryoprotectant), VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.9793 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 8, 2008 |
Radiation | Monochromator: DCM WITH CRYO-COOLED 1ST CRYSTAL, SAGITTALLY BENT 2ND CRYSTAL, FOLLOWED BY VERTICALLY FOCUSING MIRROR Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→60 Å / Num. all: 30243 / Num. obs: 30243 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.16 % / Rmerge(I) obs: 0.079 / Rsym value: 0.063 / Net I/σ(I): 23.01 |
Reflection shell | Resolution: 1.6→1.7 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.372 / Mean I/σ(I) obs: 5.34 / Num. unique all: 4938 / Rsym value: 0.529 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3O79 Resolution: 1.6→61.35 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.954 / SU B: 3.073 / SU ML: 0.05 / Isotropic thermal model: Anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.102 / ESU R Free: 0.087 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.807 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→61.35 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.642 Å / Total num. of bins used: 20
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