|Entry||Database: PDB / ID: 1xyk|
|Title||NMR Structure of the canine prion protein|
|Keywords||UNKNOWN FUNCTION / PrP / prion / Prnp / cPrP|
|Function / homology||Prion/Doppel protein, beta-ribbon domain / Prion protein / Major prion protein N-terminal domain / Prion/Doppel beta-ribbon domain superfamily / Prion/Doppel alpha-helical domain / Major prion protein bPrPp - N terminal / Prion protein signature 1. / Prion protein signature 2. / anchored component of membrane / protein homooligomerization ...Prion/Doppel protein, beta-ribbon domain / Prion protein / Major prion protein N-terminal domain / Prion/Doppel beta-ribbon domain superfamily / Prion/Doppel alpha-helical domain / Major prion protein bPrPp - N terminal / Prion protein signature 1. / Prion protein signature 2. / anchored component of membrane / protein homooligomerization / copper ion binding / Golgi apparatus / plasma membrane / Major prion protein|
Function and homology information
|Specimen source||Canis lupus familiaris (dog)|
|Method||SOLUTION NMR / torsion angle dynamics|
|Authors||Lysek, D.A. / Schorn, C. / Esteve-Moya, V. / Herrmann, T. / Wuthrich, K.|
|Citation||Journal: Proc.Natl.Acad.Sci.USA / Year: 2005|
Title: Prion protein NMR structures of cats, dogs, pigs, and sheep
Authors: Lysek, D.A. / Schorn, C. / Nivon, L.G. / Esteve-Moya, V. / Christen, B. / Calzolai, L. / von Schroetter, C. / Fiorito, F. / Herrmann, T. / Guntert, P. / Wuthrich, K.
SummaryFull reportAbout validation report
|Date||Deposition: Nov 10, 2004 / Release: Jan 4, 2005|
|Structure viewer||Molecule: |
Downloads & links
A: prion protein
|#1: Protein/peptide|| |
Mass: 13084.538 Da / Num. of mol.: 1 / Fragment: cPrP C-TERMINAL DOMAIN / Source: (gene. exp.) Canis lupus familiaris (dog) / Genus: Canis / Species: Canis lupus / Strain: familiaris / Genus (production host): Escherichia / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: O46501
|Experiment||Method: SOLUTION NMR|
|NMR details||Text: This structure was determined using standard 3D techniques|
|Details||Contents: 1mM cPrP U-15N, 13C; 10mM acetate / Solvent system: 90% H2O/10% D2O|
|sample conditions||Ionic strength: 10 / pH: 4.5 / Pressure: ambient / Temperature: 293 K|
|Radiation||Diffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M|
|Radiation wavelength||Relative weight: 1|
|NMR spectrometer||Type: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 750 MHz|
|Refinement||Method: torsion angle dynamics / Software ordinal: 1|
|NMR representative||Selection criteria: fewest violations|
|NMR ensemble||Conformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20|
-Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)
EMDB accession codes are about to change! (news from PDBe EMDB page)
- The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force. (see PDBe EMDB page)
- The EM Navigator/Yorodumi systems omit the EMD- prefix.
Related info.: Q: What is "EMD"? / ID/Accession-code notation in Yorodumi/EM Navigator
-Jul 12, 2017. Major update of PDB
Major update of PDB
- wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary. This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated. See below links for details.
- In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software). Now, EM Navigator and Yorodumi are based on the updated data.
+Jun 16, 2017. Omokage search with filter
Omokage search with filter
- Result of Omokage search can be filtered by keywords and the database types
Related info.: Omokage search
+Sep 15, 2016. EM Navigator & Yorodumi renewed
EM Navigator & Yorodumi renewed
- New versions of EM Navigator and Yorodumi started
Related info.: Changes in new EM Navigator and Yorodumi
+Aug 31, 2016. New EM Navigator & Yorodumi
New EM Navigator & Yorodumi
- In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
- Current version will continue as 'legacy version' for some time.
Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi
Thousand views of thousand structures
- Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
- This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
Related info.: EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi