[English] 日本語
Yorodumi
- PDB-1tt3: NMR soulution structure of omega-conotoxin [K10]MVIIA -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1tt3
TitleNMR soulution structure of omega-conotoxin [K10]MVIIA
ComponentsOmega-conotoxin MVIIa
KeywordsTOXIN / cysteine knot / four loop frame work
Function / homology
Function and homology information


host cell presynaptic membrane / ion channel inhibitor activity / calcium channel regulator activity / toxin activity / extracellular region
Similarity search - Function
Conotoxin, omega-type, conserved site / Omega-conotoxin family signature. / Conotoxin / Conotoxin
Similarity search - Domain/homology
Omega-conotoxin MVIIA
Similarity search - Component
MethodSOLUTION NMR / Structures were calculated using torsion angle dynamics, simulated annealing protocol
AuthorsAdams, D.J. / Smith, A.B. / Schroeder, C.I. / Yasuda, T. / Lewis, R.J.
Citation
Journal: J.Biol.Chem. / Year: 2003
Title: omega-conotoxin CVID inhibits a pharmacologically distinct voltage-sensitive calcium channel associated with transmitter release from preganglionic nerve terminals
Authors: Adams, D.J. / Smith, A.B. / Schroeder, C.I. / Yasuda, T. / Lewis, R.J.
#1: Journal: to be published
Title: The alfa2delta auxiliary subunit reduces the affinity of omega-conotoxins for recombinant N-type calcium channels
Authors: Mould, J. / Yasuda, T. / Schroeder, C.I. / Beedle, A.M. / Doering, C.J. / Zamponi, G.W. / Adams, D.J. / Lewis, R.J.
History
DepositionJun 21, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 6, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 10, 2021Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Omega-conotoxin MVIIa


Theoretical massNumber of molelcules
Total (without water)2,6221
Polymers2,6221
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)22 / 50structures with the lowest energy
RepresentativeModel #7lowest energy

-
Components

#1: Protein/peptide Omega-conotoxin MVIIa / omega-conotoxin [K10]MVIIA


Mass: 2622.210 Da / Num. of mol.: 1 / Mutation: R10K / Source method: obtained synthetically
Details: This sequence contains a [R10K] mutation of the naturally occuring MVIIA from Conus magus
References: UniProt: P05484

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D TOCSY
1212D NOESY
131DQF-COSY
1422D TOCSY
1522D NOESY
162E-COSY

-
Sample preparation

Details
Solution-IDContentsSolvent system
12mM [K10]MVIIA, 95% H2O, 5% D2O, DSS95% H2O/5% D2O
22mM [K10]MVIIA, 100% D2O, DSS100% D2O
Sample conditions
Conditions-IDpHPressure (kPa)Temperature (K)
13.5 ambient 293 K
23.5 ambient 280 K

-
NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX5001
Bruker AMXBrukerAMX7502

-
Processing

NMR software
NameVersionClassification
XwinNMR3.5collection
X-PLOR3.851structure solution
X-PLOR3.851refinement
RefinementMethod: Structures were calculated using torsion angle dynamics, simulated annealing protocol
Software ordinal: 1
Details: A total of 479 distance restraints (including H-bonds) and 30 dihedral angle restraints (including 21 phi, 9 chi) were used to calculate the structures.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 22

+
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