[English] 日本語
Yorodumi
- PDB-1s4t: Solution structure of synthetic 21mer peptide spanning region 135... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1s4t
TitleSolution structure of synthetic 21mer peptide spanning region 135-155 (in human numbering) of sheep prion protein
ComponentsMajor prion protein
KeywordsUNKNOWN FUNCTION / prion / helix
Function / homology
Function and homology information


side of membrane / tubulin binding / protein homooligomerization / microtubule binding / copper ion binding / Golgi apparatus / identical protein binding / plasma membrane
Similarity search - Function
Prion protein signature 1. / Prion protein signature 2. / Major prion protein N-terminal domain / Major prion protein bPrPp - N terminal / 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
MethodSOLUTION NMR / Molecular dynamics with AMBER99 all-atom force field parameters by using the variable target function approach in the torsion angle space with the standard geometry of amino acids, peptide bonds.
AuthorsKozin, S.A. / Lepage, C. / Hui Bon Hoa, G. / Rabesona, H. / Mazur, A.K. / Blond, A. / Cheminant, M. / Haertle, T. / Debey, P. / Rebuffat, S.
CitationJournal: To be Published
Title: Specific recognition between surface loop 2 (132-143) and helix 1 (144-154) within sheep prion protein from in vitro studies of synthetic peptides
Authors: Kozin, S.A. / Lepage, C. / Hui Bon Hoa, G. / Rabesona, H. / Mazur, A.K. / Blond, A. / Cheminant, M. / Haertle, T. / Debey, P. / Rebuffat, S.
History
DepositionJan 18, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 27, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Major prion protein


Theoretical massNumber of molelcules
Total (without water)2,7431
Polymers2,7431
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 1000The submitted conformer models are the 20 structures with the least restraint violations and the lowestt energy
RepresentativeModel #1closest to the average

-
Components

#1: Protein/peptide Major prion protein / PrP


Mass: 2742.977 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: This peptide has been chemically synthesized. The sequence occurs naturally in sheep.
References: UniProt: P23907

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentType: 2D NOESY
NMR detailsText: This structure was determined using standard 2D homonuclear techniques.

-
Sample preparation

DetailsContents: 5 mM / Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: nd / pH: 2.3 / Pressure: ambient / Temperature: 324 K

-
NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 400 MHz

-
Processing

NMR software
NameVersionDeveloperClassification
XwinNMR1.3Brukercollection
AURELIA2.5.9Brukerprocessing
ICMDy2.3Mazur, A.K.structure solution
ICMDy2.3Mazur, A.K.refinement
RefinementMethod: Molecular dynamics with AMBER99 all-atom force field parameters by using the variable target function approach in the torsion angle space with the standard geometry of amino acids, peptide bonds.
Software ordinal: 1
Details: The structures are based on a total of 134 NOE-derived distance constraints.
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: The submitted conformer models are the 20 structures with the least restraint violations and the lowestt energy
Conformers calculated total number: 1000 / Conformers submitted total number: 20

+
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