[English] 日本語
Yorodumi
- PDB-2sh1: SOLUTION STRUCTURE OF NEUROTOXIN I FROM THE SEA ANEMONE STICHODAC... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2sh1
TitleSOLUTION STRUCTURE OF NEUROTOXIN I FROM THE SEA ANEMONE STICHODACTYLA HELIANTHUS. A NUCLEAR MAGNETIC RESONANCE, DISTANCE GEOMETRY AND RESTRAINED MOLECULAR DYNAMICS STUDY
ComponentsNEUROTOXIN I
KeywordsNEUROTOXIN
Function / homology
Function and homology information


nematocyst / sodium channel regulator activity / regulation of signal transduction / toxin activity / extracellular region
Similarity search - Function
Sea anemone toxin / Anenome neurotoxin / Anthopleurin-A / Myotoxin/Anemone neurotoxin domain superfamily / Anthopleurin-A / Single Sheet / Mainly Beta
Similarity search - Domain/homology
Delta-stichotoxin-She1a
Similarity search - Component
Biological speciesStichodactyla helianthus (sea anemone)
MethodSOLUTION NMR
AuthorsFogh, R.H. / Norton, R.S.
Citation
Journal: J.Biol.Chem. / Year: 1990
Title: Solution structure of neurotoxin I from the sea anemone Stichodactyla helianthus. A nuclear magnetic resonance, distance geometry, and restrained molecular dynamics study.
Authors: Fogh, R.H. / Kem, W.R. / Norton, R.S.
#1: Journal: Biochemistry / Year: 1989
Title: Sequence-Specific 1H NMR Assignments and Secondary Structure in the Sea Anemone Polypeptide Stichodactyla Helianthus Neurotoxin I
Authors: Fogh, R.H. / Mabbutt, B.C. / Kem, W.R. / Norton, R.S.
History
DepositionMay 3, 1990Processing site: BNL
Revision 1.0Oct 15, 1991Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / pdbx_struct_assembly ...pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conf
Item: _pdbx_database_status.process_site
Revision 1.4Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: NEUROTOXIN I


Theoretical massNumber of molelcules
Total (without water)5,1501
Polymers5,1501
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Atom site foot note1: THE POSITIONS OF ALL ATOMS IN THE LOOP BETWEEN ASP 7 CA AND PRO 16 CA, AS WELL AS IN LYS 48, ARE ESSENTIALLY UNCONSTRAINED BY THE INPUT DATA AND SHOULD BE REGARDED AS UNDEFINED.
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)8 / -
Representative

-
Components

#1: Protein/peptide NEUROTOXIN I


Mass: 5149.879 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Stichodactyla helianthus (sea anemone) / References: UniProt: P19651
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR

-
Sample preparation

Crystal grow
*PLUS
Method: other / Details: NMR

-
Processing

NMR software
NameDeveloperClassification
DISMANBRAUN,GOrefinement
DISGEOHAVEL,WUTHRICHrefinement
GROMOS-87VAN GUNSTEREN,BERENDSENrefinement
NMR ensembleConformers submitted total number: 8

+
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