[English] 日本語
Yorodumi
- PDB-1t50: NMR SOLUTION STRUCTURE OF APLYSIA ATTRACTIN -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1t50
TitleNMR SOLUTION STRUCTURE OF APLYSIA ATTRACTIN
ComponentsAttractin
KeywordsATTRACTIN / MOLLUSK / PHEROMONE / APLYSIA ATTRACTIN
Function / homology
Function and homology information


mating pheromone activity / sexual reproduction / extracellular region
Similarity search - Function
Mollusk pheromone / Attractin / Attractin / Attractin superfamily / Attractin family / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesAplysia californica (California sea hare)
MethodSOLUTION NMR / SELF-CORRECTING DG, VTF
AuthorsRavindranath, G. / Xu, Y. / Schein, C.H. / Rajaratnam, K. / Painter, S.D. / Nagle, G.T. / Braun, W.
Citation
Journal: Biochemistry / Year: 2003
Title: NMR Solution Structure of Attractin, a Water-Borne Pheromone from the Mollusk Aplysia Attractin
Authors: Ravindranath, G. / Xu, Y. / Schein, C.H. / Rajarathnam, K. / Nagle, G.T. / Painter, S.D. / Braun, W.
#1: Journal: Biophys.J. / Year: 2001
Title: Aplysia Attractin: Biophysical Characterization and Modeling of a Water-Borne Pheromone
Authors: Schein, C.H. / Nagle, G.T. / Page, J.S. / Sweedler, J.V. / Xu, Y. / Painter, S.D. / Braun, W.
History
DepositionApr 30, 2004Deposition site: RCSB / Processing site: RCSB
SupersessionMay 11, 2004ID: 1NJ7
Revision 1.0May 11, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Attractin


Theoretical massNumber of molelcules
Total (without water)6,3601
Polymers6,3601
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 50VTF VALUES
RepresentativeModel #1closest to the average

-
Components

#1: Protein Attractin


Mass: 6359.892 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aplysia californica (California sea hare)
Description: Sf-900 II serum-free medium / Gene: ATT / Cell line (production host): SF9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: O96910

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111NOESY
121TOCSY
131DQF-COSY
NMR detailsText: HOMONUCLEAR 1H NMR SPECTROSCOPY

-
Sample preparation

DetailsContents: 0.7mM Unlabled protein, 10 mM sodium phosphate buffer, 90% H20, 10% D20
Solvent system: 90% H20, 10% D20
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
11 mM 6.8 ambient 298 K
21 mM 6.8 ambient 288 K

-
NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Varian UNITYPLUS / Manufacturer: Varian / Model: UNITYPLUS / Field strength: 600 MHz

-
Processing

NMR software
NameClassification
NOAH/DIAMONDstructure solution
FANTOMrefinement
RefinementMethod: SELF-CORRECTING DG, VTF / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: VTF VALUES / Conformers calculated total number: 50 / 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://pdbjlvh1.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