[English] 日本語
Yorodumi
- PDB-6cuc: Solution structure of double knot toxin (DkTx) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6cuc
TitleSolution structure of double knot toxin (DkTx)
ComponentsTau-theraphotoxin-Hs1a
KeywordsTOXIN / ICK / spider toxin / dktx / trpv1 / tarantula
Function / homologyion channel regulator activity / toxin activity / lipid binding / extracellular region / Tau-theraphotoxin-Hs1a
Function and homology information
Biological speciesHaplopelma schmidti (Chinese earth tiger)
MethodSOLUTION NMR / simulated annealing
AuthorsRamanujam, V. / Mobli, M.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2024
Title: Structural Basis of the Bivalency of the TRPV1 Agonist DkTx.
Authors: Ramanujam, V. / Crawford, T. / Cristofori-Armstrong, B. / Deuis, J.R. / Jia, X. / Maxwell, M.J. / Jami, S. / Ma, L. / Vetter, I. / Mobli, M.
History
DepositionMar 25, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 27, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_spectrometer / struct_conn
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_conn.pdbx_dist_value
Revision 1.2Apr 24, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Tau-theraphotoxin-Hs1a


Theoretical massNumber of molelcules
Total (without water)9,2881
Polymers9,2881
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 20all calculated structures submitted
RepresentativeModel #1medoid

-
Components

#1: Protein Tau-theraphotoxin-Hs1a / Tau-TRTX-Hs1a / Double-knot toxin / DkTx


Mass: 9287.728 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haplopelma schmidti (Chinese earth tiger)
Production host: Escherichia coli (E. coli) / References: UniProt: P0CH43

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
121isotropic13D HNCO
131isotropic13D CBCA(CO)NH
141isotropic13D HN(CA)CB
151isotropic13D HBHA(CO)NH
161isotropic13D (H)CCH-TOCSY
171isotropic13D 1H-13C NOESY aliphatic
181isotropic13D 1H-13C NOESY aromatic
191isotropic13D 1H-15N NOESY

-
Sample preparation

DetailsType: solution
Contents: 300 uM [U-13C; U-15N] DkTx, 20 mM sodium phosphate, 10 uM DSS, 0.02 % w/v sodium azide, 95% H2O/5% D2O
Label: 13C/15N sample / Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
300 uMDkTx[U-13C; U-15N]1
20 mMsodium phosphatenatural abundance1
10 uMDSSnatural abundance1
0.02 % w/vsodium azidenatural abundance1
Sample conditionsIonic strength: 0 Not defined / Label: conditions_1 / pH: 5.8 / PH err: 0.05 / Pressure: ambient / Temperature: 298 K

-
NMR measurement

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

-
Processing

NMR software
NameDeveloperClassification
CYANAGuntert P.refinement
CcpNMRCCPNdata analysis
RNMRTKHoch and Sternprocessing
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: medoid
NMR ensembleConformer selection criteria: all calculated structures submitted
Conformers calculated total number: 20 / 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