[English] 日本語
Yorodumi
- PDB-5i2p: Resonance assignments and NMR structure determination of tarantul... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5i2p
TitleResonance assignments and NMR structure determination of tarantula toxin- W7A mutant of mu-TRTX-Pre1a (W6A in native sequence numbering)
ComponentsW7A mu-TRTX-Pre1a Toxin
KeywordsTOXIN / Spider toxin / Voltage-gated sodium channel modulator / Inhibitor cystein knot / disulfide-rich
Function / homologyHuwentoxin-1 family / Ion channel inhibitory toxin / ion channel inhibitor activity / sodium channel regulator activity / toxin activity / extracellular region / Beta/delta-theraphotoxin-Pre1a
Function and homology information
Biological speciesPsalmopoeus (spider)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsChin, Y.K.-Y. / Wingerd, J.S. / Mobli, M. / Rash, L.D.
CitationJournal: To Be Published
Title: Resonance assignments and NMR structure determination of tarantula toxin- W7A mutant of mu-TRTX-Pre1a
Authors: Wingerd, J.S. / Chin, Y.K.-Y. / Cristofori-Armstrong, B. / Mobli, M. / Rash, L.D.
History
DepositionFeb 9, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 28, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer
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_software.name / _pdbx_nmr_spectrometer.model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: W7A mu-TRTX-Pre1a Toxin


Theoretical massNumber of molelcules
Total (without water)4,2151
Polymers4,2151
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 30structures with acceptable covalent geometry
RepresentativeModel #1lowest energy

-
Components

#1: Protein/peptide W7A mu-TRTX-Pre1a Toxin


Mass: 4214.890 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Psalmopeus reduncus / Source: (gene. exp.) Psalmopoeus (spider) / Plasmid: pLICC
Details (production host): Periplasmic expression vector for expression of toxin with C-terminal His6 tagged MBP and a TEV cleavage site in between
Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: A0A1S4NYE8*PLUS

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
121isotropic13D CBCA(CO)NH
131isotropic13D HNCO
141isotropic13D HN(CA)CB
151isotropic13D 1H-15N NOESY
1101isotropic13D HBHA(CO)NH
191isotropic13D 1H-13C NOESY aliphatic
181isotropic13D 1H-13C NOESY aromatic
171isotropic14D HCC(co)NH-TOCSY
NMR detailsText: Best stereochemical properties judged by Molprobity

-
Sample preparation

DetailsType: solution
Contents: 300 uM [U-99% 13C; U-99% 15N] W7A-mu-TRTX-Pre1a, 10 mM sodium phosphate, 5 % D2O, 95% H2O/5% D2O
Label: CN labelled W7A pre1a / Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
300 uMW7A-mu-TRTX-Pre1a[U-99% 13C; U-99% 15N]1
10 mMsodium phosphatenatural abundance1
5 %D2Onatural abundance1
Sample conditionsIonic strength: 10 mM / Label: condition1 / pH: 6 / Pressure: 1 atm / Temperature: 298 K

-
NMR measurement

NMR spectrometerType: Bruker AVANCE II / Manufacturer: Bruker / Model: AVANCE II / Field strength: 900 MHz / Details: nmr900

-
Processing

NMR software
NameDeveloperClassification
CcpNMRCCPNchemical shift assignment
CYANAGuntert, Mumenthaler and Wuthrichrefinement
TopSpinBruker Biospincollection
CcpNMRCCPNpeak picking
Rowland NMR ToolkitJeff Hochprocessing
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
RefinementMethod: torsion angle dynamics / Software ordinal: 2
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with acceptable covalent geometry
Conformers calculated total number: 30 / 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