[English] 日本語
Yorodumi
- PDB-1i25: Three dimensional solution structure of huwentoxin-II by 2D 1H-NMR -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1i25
TitleThree dimensional solution structure of huwentoxin-II by 2D 1H-NMR
ComponentsHUWENTOXIN-II
KeywordsTOXIN / neurotoxin / insecticidal toxin / disulfide bonds
Function / homologyHuwentoxin-II family / Huwentoxin-II family / Huwentoxin-2 family signature. / host cell postsynaptic membrane / toxin activity / extracellular region / U1-theraphotoxin-Hs1a
Function and homology information
Biological speciesOrnithoctonus huwena (Chinese earth tiger)
MethodSOLUTION NMR / simulated annealing
AuthorsShu, Q. / Lu, S.Y. / Gu, X.C. / Liang, S.P.
Citation
Journal: Protein Sci. / Year: 2002
Title: The structure of spider toxin huwentoxin-II with unique disulfide linkage: evidence for structural evolution.
Authors: Shu, Q. / Lu, S.Y. / Gu, X.C. / Liang, S.P.
#1: Journal: ACTA BIOCHIM.BIOPHYS.SINICA / Year: 2001
Title: Sequence-specific Assignment of 1H-NMR Resonance and Determination of the Secondary Structure of HWTX-II
Authors: Shu, Q. / Lu, S.Y. / Gu, X.C. / Liang, S.P.
#2: Journal: To be Published
Title: Assignment of Disulfide Bonds of Huwentoxin-II by Edman Degradation Sequencing and Stepwise Thiol Modification
Authors: Shu, Q. / Huang, R.H. / Liang, S.P.
#3: Journal: J.PEPT.RES. / Year: 1999
Title: Purification and Characterization of Huwentoxin-II, a Neurotoxic Peptide from the Venom of the Chinese Bird Spider Selenocosmia huwena
Authors: Shu, Q. / Liang, S.P.
History
DepositionFeb 6, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 14, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_oper_list / struct_conf
Revision 1.4Nov 6, 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 / pdbx_nmr_software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
Remark 750TURN DETERMINATION METHOD: AUTHOR-DETERMINED

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: HUWENTOXIN-II


Theoretical massNumber of molelcules
Total (without water)4,3001
Polymers4,3001
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 50structures with the lowest energy
RepresentativeModel #1closest to the average

-
Components

#1: Protein/peptide HUWENTOXIN-II / HWTX-II


Mass: 4300.246 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: VENOM
Source: (natural) Ornithoctonus huwena (Chinese earth tiger)
Organ: VENOM GLAND / References: UniProt: P82959
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111NOESY
121DQF-COSY
131TOCSY
142NOESY
152E-COSY
162TOCSY
271NOESY
281TOCSY
NMR detailsText: This structure was determined using standard 2D homonuclear techniques.

-
Sample preparation

Details
Solution-IDContentsSolvent system
14 mM Huwentoxin-II; 20 mmol/l phosphate buffer; 90%H2O , 10%D2O90% H2O/10% D2O
24 mM Huwentoxin-II; 20 mmol/l phosphate buffer; 100%D2O100% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
1205.41 atm300 K
25.41 atm290 K
Crystal grow
*PLUS
Method: other / Details: NMR

-
NMR measurement

NMR spectrometerType: Bruker DMX / Manufacturer: Bruker / Model: DMX / Field strength: 500 MHz

-
Processing

NMR software
NameVersionDeveloperClassification
Felix98Molecular Simulations, Inc.data analysis
X-PLOR3.851Brungerrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: The structures are based on 592 NOE-derived distance constraints, 16 dihedral angel restraints and 9 fake distance restraints from disulfide bonds.
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 10

+
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