[English] 日本語
Yorodumi
- PDB-8uwf: NMR structure of the funnel-web spider toxin Hc3a -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8uwf
TitleNMR structure of the funnel-web spider toxin Hc3a
ComponentsPi-Hexatoxin-Hc1b_1
KeywordsTOXIN / Inhibitor cystine knot / Acid-sensing ion channel
Function / homologyion channel inhibitor activity / extracellular region / Pi-Hexatoxin-Hc1b_1
Function and homology information
Biological speciesHadronyche cerberea (spider)
MethodSOLUTION NMR / simulated annealing
AuthorsBudusan, E. / Payne, C.D. / Gonzalez, T.I. / Clark, R.J. / Rosengren, K.J. / Rash, L.D. / Cristofori-Armstrong, B.
Funding support Australia, 2items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)APP1162597 Australia
National Health and Medical Research Council (NHMRC, Australia)APP1162427 Australia
CitationJournal: Biochem Pharmacol / Year: 2024
Title: The funnel-web spider venom derived single knot peptide Hc3a modulates acid-sensing ion channel 1a desensitisation.
Authors: Budusan, E. / Payne, C.D. / Gonzalez, T.I. / Obergrussberger, A. / Becker, N. / Clark, R.J. / Johan Rosengren, K. / Rash, L.D. / Cristofori-Armstrong, B.
History
DepositionNov 6, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 13, 2024Provider: repository / Type: Initial release
Revision 1.1Apr 10, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2May 15, 2024Group: Database references / Category: database_2 / Item: _database_2.pdbx_DOI

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Pi-Hexatoxin-Hc1b_1


Theoretical massNumber of molelcules
Total (without water)4,4951
Polymers4,4951
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: NMR Distance Restraints, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with acceptable covalent geometry
RepresentativeModel #1best molprobity score

-
Components

#1: Protein/peptide Pi-Hexatoxin-Hc1b_1


Mass: 4495.241 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hadronyche cerberea (spider) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A4Q8K7H6

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-1H TOCSY
121isotropic12D 1H-1H NOESY
131isotropic12D 1H-13C HSQC
141isotropic12D 1H-15N HSQC
251isotropic12D 1H-1H TOCSY
361isotropic12D 1H-1H TOCSY
471isotropic12D 1H-1H TOCSY
581isotropic12D 1H-1H TOCSY

-
Sample preparation

DetailsType: solution / Contents: 4 mg/mL Hc3a, 90% H2O/10% D2O / Label: Hc3a / Solvent system: 90% H2O/10% D2O
SampleConc.: 4 mg/mL / Component: Hc3a / Isotopic labeling: natural abundance
Sample conditions
Conditions-IDIonic strengthLabelpHPressure (kPa)Temperature (K)
10 mMStandard3.5 1 atm298 K
20 mMStandard3.5 1 atm288 K
30 mMStandard3.5 1 atm293 K
40 mMStandard3.5 1 atm303 K
50 mMStandard3.5 1 atm308 K

-
NMR measurement

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

-
Processing

NMR software
NameDeveloperClassification
CARAKeller and Wuthrichchemical shift assignment
CARAKeller and Wuthrichpeak picking
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
CYANAGuntert, Mumenthaler and Wuthrichrefinement
MolProbityRichardsondata analysis
RefinementMethod: simulated annealing / Software ordinal: 5 / Details: Simulated annealing using torsion angle dynamics
NMR representativeSelection criteria: best molprobity score
NMR ensembleConformer selection criteria: structures with acceptable covalent geometry
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