[English] 日本語
Yorodumi
- PDB-1tor: MOLECULAR DYNAMICS SIMULATION FROM 2D-NMR DATA OF THE FREE ACHR M... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1tor
TitleMOLECULAR DYNAMICS SIMULATION FROM 2D-NMR DATA OF THE FREE ACHR MIR DECAPEPTIDE AND THE ANTIBODY-BOUND [A76]MIR ANALOGUE
ComponentsACETYLCHOLINE RECEPTOR, MAIN IMMUNOGENIC REGION
KeywordsTRANSMEMBRANE PROTEIN
Function / homology
Function and homology information


acetylcholine-gated monoatomic cation-selective channel activity / transmembrane signaling receptor activity / postsynaptic membrane / neuron projection
Similarity search - Function
Nicotinic acetylcholine receptor / Neurotransmitter-gated ion-channel, conserved site / Neurotransmitter-gated ion-channels signature. / Neurotransmitter-gated ion-channel transmembrane domain / Neurotransmitter-gated ion-channel transmembrane region / Neurotransmitter-gated ion-channel transmembrane domain superfamily / Neuronal acetylcholine receptor / Neurotransmitter-gated ion-channel / Neurotransmitter-gated ion-channel ligand-binding domain / Neurotransmitter-gated ion-channel ligand-binding domain superfamily / Neurotransmitter-gated ion-channel ligand binding domain
Similarity search - Domain/homology
Acetylcholine receptor subunit alpha
Similarity search - Component
Biological speciesTorpedo californica (Pacific electric ray)
MethodSOLUTION NMR
AuthorsOrlewski, P. / Tsikaris, V. / Sakarellos, C. / Sakarellos-Daistiotis, M. / Vatzaki, E. / Tzartos, S.J. / Marraud, M. / Cung, M.T.
Citation
Journal: Biopolymers / Year: 1996
Title: Compared structures of the free nicotinic acetylcholine receptor main immunogenic region (MIR) decapeptide and the antibody-bound [A76]MIR analogue: a molecular dynamics simulation from two-dimensional NMR data.
Authors: Orlewski, P. / Marraud, M. / Cung, M.T. / Tsikaris, V. / Sakarellos-Daitsiotis, M. / Sakarellos, C. / Vatzaki, E. / Tzartos, S.J.
#1: Journal: Biopolymers / Year: 1993
Title: Conformational Requirements for Molecular Recognition of Acetylcholine Receptor Main Immunogenic Region (Mir) Analogues by Monoclonal Anti-Mir Antibody: A Two-Dimensional Nuclear Magnetic ...Title: Conformational Requirements for Molecular Recognition of Acetylcholine Receptor Main Immunogenic Region (Mir) Analogues by Monoclonal Anti-Mir Antibody: A Two-Dimensional Nuclear Magnetic Resonance and Molecular Dynamics Approach
Authors: Tsikaris, V. / Desticas, E. / Sakarellos-Daistiotis, M. / Sakarellos, C. / Cung, M.T. / Marraud, M. / Vatzaki, E. / Tzartos, S.J.
#2: Journal: Pept.Res. / Year: 1992
Title: 2D-NMR and Molecular Dynamics Analysis of the Torpedo Californica Acetylcholine Receptor Alpha67-76 Fragment and of its [Ala76]-Analogue
Authors: Cung, M.T. / Tsikaris, V. / Demange, P. / Papadouli, I. / Tzartos, S. / Sakarellos, C. / Marraud, M.
#3: Journal: Biopolymers / Year: 1991
Title: Two-Dimensional 1H-NMR Study of Antigen-Antibody Interactions: Binding of Synthetic Decapeptides to an Anti-Acetylcholine Receptor Monoclonal Antibody
Authors: Cung, M.T. / Demange, P. / Marraud, M. / Tsikaris, V. / Papadouli, I. / Sakarellos, C. / Kokla, A. / Tzartos, S.J.
#4: Journal: Biopolymers / Year: 1989
Title: Two-Dimensional 1H-NMR Study of Synthetic Peptides Containing the Main Immunogenic Region of the Torpedo Acetylcholine Receptor
Authors: Cung, M.T. / Marraud, M. / Hadjidakis, I. / Bairaktari, E. / Sakarellos, C. / Kokla, A. / J Tzartos, S.
History
DepositionOct 11, 1995Processing site: BNL
Revision 1.0Mar 8, 1996Provider: 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
Item: _pdbx_database_status.process_site
Revision 1.4May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: ACETYLCHOLINE RECEPTOR, MAIN IMMUNOGENIC REGION


Theoretical massNumber of molelcules
Total (without water)1,1211
Polymers1,1211
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)5 / -
Representative

-
Components

#1: Protein/peptide ACETYLCHOLINE RECEPTOR, MAIN IMMUNOGENIC REGION / MIR


Mass: 1121.223 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Torpedo californica (Pacific electric ray)
References: UniProt: P02710

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR

-
Sample preparation

Crystal grow
*PLUS
Method: other

-
Processing

NMR software
NameVersionDeveloperClassification
DGIIHAVELrefinement
Discover2.8BIOSYMrefinement
NMR ensembleConformers submitted total number: 5

+
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