[English] 日本語
Yorodumi
- SASDEX7: C-terminal truncated bank vole prion protein (amino acids 90-231)... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: SASBDB / ID: SASDEX7
SampleC-terminal truncated bank vole prion protein (amino acids 90-231) bound to Cu(II)
  • Major prion protein (protein), Myodes glareolus
Function / homology
Function and homology information


side of membrane / protein homooligomerization / Golgi apparatus / metal ion binding / plasma membrane
Similarity search - Function
Prion, copper binding octapeptide repeat / Copper binding octapeptide repeat region / Major prion protein N-terminal domain / Major prion protein bPrPp - N terminal / Prion protein signature 1. / Prion protein signature 2. / Prion protein / Major prion protein / Prion/Doppel protein, beta-ribbon domain / Prion/Doppel beta-ribbon domain superfamily / Prion/Doppel alpha-helical domain
Similarity search - Domain/homology
Biological speciesMyodes glareolus (Bank vole)
Contact author
  • Gabriele Giachin (ESRF, European Synchrotron Radiation Facility, Grenoble, France)

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Models

Model #2620
Type: mix / Symmetry: P1 / Chi-square value: 1.275 / P-value: 0.215624
Search similar-shape structures of this assembly by Omokage search (details)

-
Sample

SampleName: C-terminal truncated bank vole prion protein (amino acids 90-231) bound to Cu(II)
Specimen concentration: 10 mg/ml
BufferName: 25 mM Ammonium Acetate, 250 mM NaCl, 0.001 mM CuSO4 / pH: 5.5
Entity #1371Type: protein / Description: Major prion protein / Formula weight: 16.14 / Num. of mol.: 1 / Source: Myodes glareolus / References: UniProt: Q8VHV5
Sequence:
GQGGGTHNQW NKPSKPKTNM KHVAGAAAAG AVVGGLGGYM LGSAMSRPMI HFGNDWEDRY YRENMNRYPN QVYYRPVDQY NNQNNFVHDC VNITIKQHTV TTTTKGENFT ETDVKMMERV VEQMCVTQYQ KESQAYYEGR SS

-
Experimental information

BeamInstrument name: ESRF BM29 / City: Grenoble / 国: France / Type of source: X-ray synchrotron / Wavelength: 0.099 Å / Dist. spec. to detc.: 2.864 mm
DetectorName: Pilatus 1M / Type: Dectris / Pixsize x: 172 mm
Scan
Title: C-terminal truncated bank vole prion protein (amino acids 90-231) bound to Cu(II)
Measurement date: Feb 25, 2018 / Storage temperature: 20 °C / Cell temperature: 20 °C / Exposure time: 1 sec. / Number of frames: 1 / Unit: 1/nm /
MinMax
Q0.1077 4.9277
Distance distribution function P(R)
Sofotware P(R): GNOM 5.0 / Number of points: 700 /
MinMax
Q0.276615 3.55725
P(R) point1 700
R0 8.7
Result
Type of curve: sec
ExperimentalStandardPorod
MW16.3 kDa15.3 kDa15.065 kDa
Volume--30.13 nm3

P(R)GuinierGuinier error
Forward scattering, I022.36 21.67 0.07
Radius of gyration, Rg2.396 nm2.2 nm0.01

MinMax
D-8.7
Guinier point54 106

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
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.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
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.
  • 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.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
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.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

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

Read more