[English] 日本語
Yorodumi
- PDB-2m36: Solution structure of the insecticidal spider-venom peptide Aps III -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2m36
TitleSolution structure of the insecticidal spider-venom peptide Aps III
ComponentsU2-cyrtautoxin-As1a
KeywordsTOXIN / Asp III / mu-CUTX-As1a / inhibitor cystine knot / voltage-gated sodium channel / insect toxin
Function / homology
Function and homology information


venom-mediated inhibition of high voltage-gated calcium channel activity / venom-mediated inhibition of low voltage-gated calcium channel activity / venom-mediated perturbation of transmission of nerve impulse / venom-mediated inhibition of voltage-gated sodium channel activity / sodium channel regulator activity / calcium channel regulator activity / toxin activity / extracellular region
Similarity search - Function
Spider insecticidal peptide / Spider insecticidal peptide
Similarity search - Domain/homology
Biological speciesApomastus schlingeri (spider)
MethodSOLUTION NMR / torsion angle dynamics
Model detailsLowest MolProbity score, model 1
AuthorsKing, G.F. / Bende, N.S. / Mobli, M.
Citation
Journal: Biochem Pharmacol / Year: 2013
Title: The insecticidal neurotoxin Aps III is an atypical knottin peptide that potently blocks insect voltage-gated sodium channels.
Authors: Bende, N.S. / Kang, E. / Herzig, V. / Bosmans, F. / Nicholson, G.M. / Mobli, M. / King, G.F.
#1: Journal: Toxicon / Year: 1992
Title: Identification of insecticidal peptides from venom of the trap-door spider, Aptostichus schlingeri (Ctenizidae).
Authors: Skinner, W.S. / Dennis, P.A. / Li, J.P. / Quistad, G.B.
History
DepositionJan 10, 2013Deposition site: BMRB / Processing site: RCSB
Revision 1.0Mar 27, 2013Provider: repository / Type: Initial release
Revision 1.1May 8, 2013Group: Database references
Revision 1.2Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.3Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: U2-cyrtautoxin-As1a


Theoretical massNumber of molelcules
Total (without water)3,8591
Polymers3,8591
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 / 200Best MolProbity scores
RepresentativeModel #1lowest molprobity score

-
Components

#1: Protein/peptide U2-cyrtautoxin-As1a / U2-CUTX-As1a / Aptotoxin III / Aptotoxin-3 / Paralytic peptide III / PP III


Mass: 3859.333 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Apomastus schlingeri (spider) / Production host: Escherichia coli (E. coli) / References: UniProt: P49268
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR / Details: Aps III
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1123D 1H-13C NOESY aliphatic
1223D 1H-13C NOESY aromatic
1313D 1H-15N NOESY
1413D HNCO
1513D HN(CA)CB
1613D CBCA(CO)NH
1713D C(CO)NH
1813D H(CCO)NH
1914D HC(CO)NH
NMR detailsText: All NMR data except NOESY experiments were acquired using nonuniform sampling and transformed using MaxEnt.

-
Sample preparation

Details
Solution-IDContentsSolvent system
1450 uM [U-100% 13C; U-100% 15N] As1a, 20 mM sodium phosphate, 95% H2O/5% D2O95% H2O/5% D2O
2450 uM [U-100% 13C; U-100% 15N] As1a, 20 mM sodium phosphate, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
450 uMAs1a-1[U-100% 13C; U-100% 15N]1
20 mMsodium phosphate-21
450 uMAs1a-3[U-100% 13C; U-100% 15N]2
20 mMsodium phosphate-42
Sample conditionspH: 6 / Pressure: ambient / Temperature: 298 K

-
NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 900 MHz

-
Processing

NMR software
NameDeveloperClassification
XEASYBartels et al.chemical shift assignment
XEASYBartels et al.peak picking
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
ProcheckNMRLaskowski and MacArthursecondary structure assignment
MolProbityDavis IW et al.analysis of stereochemical quality
TALOSCornilescu, Delaglio and Baxestimation of dihedral angles
Rowland_NMR_ToolkitHoch, Stern et al.nmr data transformation
CYANAHoch, Stern et al.refinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR constraintsNOE constraints total: 547 / NOE intraresidue total count: 117 / NOE long range total count: 171 / NOE medium range total count: 92 / NOE sequential total count: 167 / Disulfide bond constraints total count: 12 / Hydrogen bond constraints total count: 12
NMR representativeSelection criteria: lowest molprobity score
NMR ensembleConformer selection criteria: Best MolProbity scores / Conformers calculated total number: 200 / 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