[English] 日本語
Yorodumi
- PDB-1hp3: C-TERMINAL TRUNCATION OF OMEGA-ATRACOTOXIN-HV2A (CT-HV2A) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1hp3
TitleC-TERMINAL TRUNCATION OF OMEGA-ATRACOTOXIN-HV2A (CT-HV2A)
ComponentsOMEGA-ATRACOTOXIN-HV2A
KeywordsTOXIN / Cystine knot
Function / homologyOmega-atracotoxin, conserved site-2 / Omega-atracotoxin (ACTX) type 2 family signature. / Magi 5 toxic peptide / Magi 5 toxic peptide family / sodium channel inhibitor activity / calcium channel inhibitor activity / toxin activity / extracellular region / Omega-hexatoxin-Hv2a
Function and homology information
MethodSOLUTION NMR / Torsion angle dynamics, dynamical simulated annealing
AuthorsWang, X.-H. / King, G.F.
Citation
Journal: J.Biol.Chem. / Year: 2001
Title: Discovery and structure of a potent and highly specific blocker of insect calcium channels
Authors: Wang, X.-H. / Connor, M. / Wilson, D. / Wilson, H.I. / Nicholson, G.M. / Smith, R. / Shaw, D. / Mackay, J.P. / Alewood, P.F. / Christie, M.J. / King, G.F.
#1: Journal: Nat.Struct.Biol. / Year: 2000
Title: Discovery and characterization of a family of insecticidal neurotoxins with a rare vicinal disulfide bridge.
Authors: Wang, X.-H. / Connor, M. / Smith, R. / Maciejewski, M.W. / Howden, M.E.H. / Nicholson, G.M.
#2: Journal: Nat.Struct.Biol. / Year: 1997
Title: The structure of a novel insecticidal neurotoxin, omega-atracotoxin-HV1, from the venom of an Australian funnel web spider.
Authors: Fletcher, J.I. / Smith, R. / O'Donoghue, S.I. / Nilges, M. / Connor, M. / Howden, M.E. / Christie, M.J. / King, G.F.
History
DepositionDec 12, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 11, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: OMEGA-ATRACOTOXIN-HV2A


Theoretical massNumber of molelcules
Total (without water)3,3841
Polymers3,3841
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 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

-
Components

#1: Protein/peptide OMEGA-ATRACOTOXIN-HV2A / CT-HV2A


Mass: 3383.948 Da / Num. of mol.: 1 / Fragment: N-TERMINAL (RESIDUES 1-32) / Source method: obtained synthetically
Details: This sequence does not occur naturally. The peptide was chemically synthesized using standard t-Boc chemistry, and oxidized/folded in a glutathione redox buffer.
References: UniProt: P82852

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D TOCSY
1212D NOESY
1322D NOESY
NMR detailsText: This structure was determined using standard 2D homonuclear NMR techniques.

-
Sample preparation

Details
Solution-IDContentsSolvent system
12.5 mM CT-Hv2a95% H2O/5% D2O
22.5 mM CT-Hv2a100% D2O
Sample conditionsIonic strength: 0.005 / pH: 4.71 / Pressure: 1 atm / Temperature: 296 K

-
NMR measurement

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

-
Processing

NMR software
NameVersionDeveloperClassification
VNMR6.1BVariancollection
FelixFelix97Molecular Simulations, Inc.processing
X-EASY1.3.13Tai-he Xia & Christian Bartelsdata analysis
DYANA1.5Peter Guentertstructure solution
X-PLOR3.1Axel Brungerrefinement
RefinementMethod: Torsion angle dynamics, dynamical simulated annealing
Software ordinal: 1
Details: The structures are based on a total of 345 NOE-derived distance restraints, 21 dihedral-angle restraints, plus 22 restraints defining 11 hydrogen bonds.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / 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