[English] 日本語
Yorodumi
- PDB-1h5o: Solution structure of Crotamine, a neurotoxin from Crotalus duris... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1h5o
TitleSolution structure of Crotamine, a neurotoxin from Crotalus durissus terrificus
ComponentsMYOTOXIN
KeywordsTOXIN / SODIUM CHANNEL AFFECTING TOXIN / VENOM
Function / homology
Function and homology information


envenomation resulting in occlusion of the pore of voltage-gated potassium channel in another organism / defense response to fungus / potassium channel regulator activity / toxin activity / killing of cells of another organism / defense response to bacterium / extracellular region
Similarity search - Function
Myotoxin / Myotoxin, crotamine / Myotoxins signature. / Myotoxins family profile. / Anthopleurin-A / Myotoxin/Anemone neurotoxin domain superfamily / Anthopleurin-A / Single Sheet / Mainly Beta
Similarity search - Domain/homology
Crotamine / Crotamine
Similarity search - Component
Biological speciesCROTALUS DURISSUS TERRIFICUS (tropical rattlesnake)
MethodSOLUTION NMR / simulated annealing
AuthorsNicastro, G. / Franzoni, L. / De Chiara, C. / Mancin, C.A. / Giglio, J.R. / Spisni, A.
Citation
Journal: Eur.J.Biochem. / Year: 2003
Title: Solution Structure of Crotamine, a Na+ Channel Affecting Toxin from Crotalus Durissus Terrificus Venom
Authors: Nicastro, G. / Franzoni, L. / De Chiara, C. / Mancin, A.C.A. / Giglio, J.R. / Spisni, A.
#1: Journal: Toxicon / Year: 1998
Title: The Analgesic Activity of Crotamine,A Neurotoxin from Crotalus Durissus Terrificus Venom:A Biochemical and Pharmacological Study
Authors: Mancin, A.C. / Soares, A.M. / Andriao-Escarso, S.H. / Faca, V.M. / Greene, L.J. / Zuccolotto, S. / Pela, I.R. / Giglio, J.R.
History
DepositionMay 23, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 9, 2003Provider: repository / Type: Initial release
Revision 1.1Jul 24, 2013Group: Derived calculations / Other ...Derived calculations / Other / Structure summary / Version format compliance
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.
Remark 700 SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: MYOTOXIN


Theoretical massNumber of molelcules
Total (without water)4,9031
Polymers4,9031
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)26 / 50LEAST RESTRAINT VIOLATION, LEAST RESIDUAL DEVIATIONS FROM IDEALIZED GEOMETRY
Representative

-
Components

#1: Protein/peptide MYOTOXIN / CROTAMINE


Mass: 4902.878 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: VENOM OF THE RATTLESNAKE CROTALUS DURISSUS TERRIFICUS
Source: (natural) CROTALUS DURISSUS TERRIFICUS (tropical rattlesnake)
References: UniProt: P01475, UniProt: Q9PWF3*PLUS
Compound detailsEXTREMELY RAPID ACTING TOXIN THAT CAUSES MUSCLE NECROSIS. DISABLES PREY BY CAUSING INSTANTANEOUS ...EXTREMELY RAPID ACTING TOXIN THAT CAUSES MUSCLE NECROSIS. DISABLES PREY BY CAUSING INSTANTANEOUS PARALYSIS OF HIND LIMBS AND DEATH BY PARALYSIS OF THE DIAPHRAGM.

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111TOCSY
121NOESY
131DQF-COSY
NMR detailsText: THE STRUCTURE WAS DETERMINED USING HOMONUCLEAR 1H-1H 2D NMR ON THE NATURAL TOXIN EXTRACTED FROM THE SNAKE VENOM.

-
Sample preparation

DetailsContents: 1MM CROTAMINE, H2O/TFE (70/30)
Sample conditionspH: 4 / Temperature: 308 K
Crystal grow
*PLUS
Method: other / Details: NMR

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DMXBrukerDMX6001
Bruker DMXBrukerDMX8002

-
Processing

NMR software
NameVersionDeveloperClassification
DISCOVERBIOSYMrefinement
MSI DISCOVERDISCOVERstructure solution
RefinementMethod: simulated annealing / Software ordinal: 1 / Details: SEE JRNL CITATION
NMR ensembleConformer selection criteria: LEAST RESTRAINT VIOLATION, LEAST RESIDUAL DEVIATIONS FROM IDEALIZED GEOMETRY
Conformers calculated total number: 50 / Conformers submitted total number: 26

+
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