[English] 日本語
Yorodumi
- PDB-1omn: SOLUTION STRUCTURE OF OMEGA-CONOTOXIN MVIIC, A HIGH AFFINITY OF P... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1omn
TitleSOLUTION STRUCTURE OF OMEGA-CONOTOXIN MVIIC, A HIGH AFFINITY OF P-TYPE CALCIUM CHANNELS, USING 1H NMR SPECTROSCOPY AND COMPLETE RELAXATION MATRIX ANALYSIS
ComponentsOMEGA-CONOTOXIN M VII C (M SEVEN C)
KeywordsNEUROTOXIN / P-TYPE CALCIUM CHANNEL BLOCKER / CONUS VENOM / PRESYNAPTIC NEUROTOXIN / CONOTOXIN
Function / homologyConotoxin, omega-type, conserved site / Omega-conotoxin family signature. / host cell presynaptic membrane / ion channel inhibitor activity / calcium channel regulator activity / toxin activity / extracellular region / Omega-conotoxin MVIIC
Function and homology information
Biological speciesConus magus (magus cone)
MethodSOLUTION NMR
AuthorsFarr-Jones, S. / Basus, V.J.
Citation
Journal: J.Mol.Biol. / Year: 1995
Title: Solution structure of omega-conotoxin MVIIC, a high affinity ligand of P-type calcium channels, using 1H NMR spectroscopy and complete relaxation matrix analysis.
Authors: Farr-Jones, S. / Miljanich, G.P. / Nadasdi, L. / Ramachandran, J. / Basus, V.J.
#1: Journal: Neuron / Year: 1992
Title: A New Conus Peptide Ligand for Mammalian Presynaptic Ca2+ Channels
Authors: Hillyard, D.R. / Monje, V.D. / Mintz, I.M. / Cruz, L.J. / Imperial, J.S. / Olivera, B.M.
History
DepositionDec 20, 1994Processing site: BNL
Revision 1.0Dec 1, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / pdbx_struct_assembly ...pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: OMEGA-CONOTOXIN M VII C (M SEVEN C)


Theoretical massNumber of molelcules
Total (without water)2,7611
Polymers2,7611
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Atom site foot note1: LYS 2 - GLY 3 MODEL 1 OMEGA = 148.91 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
2: GLY 3 - LYS 4 MODEL 1 OMEGA = 210.78 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
3: LYS 25 - CYS 26 MODEL 1 OMEGA = 210.64 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
4: CYS 1 - LYS 2 MODEL 2 OMEGA = 210.60 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
5: ARG 9 - LYS 10 MODEL 2 OMEGA = 210.11 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
6: CYS 16 - SER 17 MODEL 2 OMEGA = 210.32 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
7: GLY 18 - SER 19 MODEL 2 OMEGA = 210.06 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
8: LYS 4 - GLY 5 MODEL 3 OMEGA = 210.33 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
9: ARG 9 - LYS 10 MODEL 3 OMEGA = 210.47 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
10: MET 12 - TYR 13 MODEL 3 OMEGA = 149.80 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
11: CYS 16 - SER 17 MODEL 3 OMEGA = 210.90 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
12: GLY 18 - SER 19 MODEL 3 OMEGA = 210.74 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
13: LYS 2 - GLY 3 MODEL 4 OMEGA = 149.39 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
14: GLY 3 - LYS 4 MODEL 4 OMEGA = 210.17 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
15: LYS 25 - CYS 26 MODEL 4 OMEGA = 210.88 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
16: GLY 3 - LYS 4 MODEL 5 OMEGA = 210.46 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
17: ARG 9 - LYS 10 MODEL 5 OMEGA = 210.13 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
18: GLY 18 - SER 19 MODEL 5 OMEGA = 210.07 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
19: LYS 25 - CYS 26 MODEL 5 OMEGA = 211.17 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
20: LYS 2 - GLY 3 MODEL 6 OMEGA = 149.18 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
21: CYS 1 - LYS 2 MODEL 7 OMEGA = 210.47 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
22: LYS 2 - GLY 3 MODEL 7 OMEGA = 148.72 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
23: GLY 3 - LYS 4 MODEL 7 OMEGA = 210.60 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
24: ARG 9 - LYS 10 MODEL 7 OMEGA = 210.28 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
25: CYS 16 - SER 17 MODEL 7 OMEGA = 210.33 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
26: LYS 25 - CYS 26 MODEL 7 OMEGA = 211.16 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
27: LYS 2 - GLY 3 MODEL 8 OMEGA = 149.60 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
28: CYS 16 - SER 17 MODEL 8 OMEGA = 210.08 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
29: ARG 9 - LYS 10 MODEL 9 OMEGA = 210.31 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
30: CYS 16 - SER 17 MODEL 9 OMEGA = 210.41 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
31: CYS 1 - LYS 2 MODEL 10 OMEGA = 210.21 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
32: LYS 2 - GLY 3 MODEL 10 OMEGA = 148.67 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
33: GLY 3 - LYS 4 MODEL 10 OMEGA = 210.30 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
34: ARG 9 - LYS 10 MODEL 10 OMEGA = 210.46 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
35: CYS 20 - GLY 21 MODEL 10 OMEGA = 210.21 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
36: LYS 25 - CYS 26 MODEL 10 OMEGA = 210.35 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
37: LYS 2 - GLY 3 MODEL 11 OMEGA = 149.99 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
38: SER 17 - GLY 18 MODEL 11 OMEGA = 210.04 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
39: ARG 9 - LYS 10 MODEL 12 OMEGA = 210.13 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
40: LYS 25 - CYS 26 MODEL 12 OMEGA = 211.32 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
41: LYS 2 - GLY 3 MODEL 13 OMEGA = 149.83 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
42: GLY 3 - LYS 4 MODEL 13 OMEGA = 210.39 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
43: ARG 9 - LYS 10 MODEL 13 OMEGA = 210.20 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
44: LYS 25 - CYS 26 MODEL 13 OMEGA = 210.60 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
45: ARG 9 - LYS 10 MODEL 14 OMEGA = 210.52 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
46: ASP 14 - CYS 15 MODEL 14 OMEGA = 210.33 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
47: CYS 16 - SER 17 MODEL 15 OMEGA = 210.45 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)15 / -
Representative

-
Components

#1: Protein/peptide OMEGA-CONOTOXIN M VII C (M SEVEN C) / SNX-230


Mass: 2761.348 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Conus magus (magus cone) / Organ: VENOM DUCT / References: UniProt: P37300

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR

-
Sample preparation

Crystal grow
*PLUS
Method: other

-
Processing

SoftwareName: AMBER / Classification: refinement
NMR softwareName: AMBER / Version: 4.1
Developer: PEARLMAN,CASE,CALDWELL,SEIBEL,SINGH,WEINER,KOLLMAN
Classification: refinement
NMR ensembleConformers submitted total number: 15

+
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://pdbjlvh1.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