[English] 日本語
Yorodumi
- PDB-1dxz: M2 TRANSMEMBRANE SEGMENT OF ALPHA-SUBUNIT OF NICOTINIC ACETYLCHOL... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1dxz
TitleM2 TRANSMEMBRANE SEGMENT OF ALPHA-SUBUNIT OF NICOTINIC ACETYLCHOLINE RECEPTOR FROM TORPEDO CALIFORNICA, NMR, 20 STRUCTURES
ComponentsACETYLCHOLINE RECEPTOR PROTEIN, ALPHA CHAIN
KeywordsTRANSMEMBRANE PROTEIN / NICOTINIC ACETYLCHOLINE RECEPTOR / TRANSMEMBRANE SEGMENT / M2 / ION-CHANNEL
Function / homology
Function and homology information


acetylcholine-gated monoatomic cation-selective channel activity / transmembrane signaling receptor activity / postsynaptic membrane
Similarity search - Function
Nicotinic acetylcholine receptor / Neurotransmitter-gated ion-channel transmembrane domain / Neurotransmitter-gated ion-channel transmembrane region / Neurotransmitter-gated ion-channel, conserved site / Neurotransmitter-gated ion-channels signature. / 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 / distance geometry
AuthorsPashkov, V.S. / Maslennikov, I.V. / Tchikin, L.D. / Efremov, R.G. / Ivanov, V.T. / Arseniev, A.S.
CitationJournal: FEBS Lett. / Year: 1999
Title: Spatial Structure of the M2 Transmembrane Segment of the Nicotinic Acetylcholine Receptor Alpha-Subunit
Authors: Pashkov, V.S. / Maslennikov, I.V. / Tchikin, L.D. / Efremov, R.G. / Ivanov, V.T. / Arseniev, A.S.
History
DepositionJan 20, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 2, 2000Provider: repository / Type: Initial release
Revision 1.1May 7, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / pdbx_nmr_software / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_mr / _pdbx_entry_details.has_protein_modification / _pdbx_nmr_software.name / _struct_conn.pdbx_leaving_atom_flag

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: ACETYLCHOLINE RECEPTOR PROTEIN, ALPHA CHAIN


Theoretical massNumber of molelcules
Total (without water)3,4161
Polymers3,4161
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 300LEAST RESTRAINTS VIOLATION
RepresentativeModel #4

-
Components

#1: Protein/peptide ACETYLCHOLINE RECEPTOR PROTEIN, ALPHA CHAIN


Mass: 3416.075 Da / Num. of mol.: 1 / Fragment: M2 TRANSMEMBRANE SEGMENT / Source method: obtained synthetically
Details: THE C-TERMINAL RESIDUE OF THE PEPTIDE IS AMIDATED. THE COMPLETE RECEPTOR CONSISTS OF A PENTAMER OF TWO ALPHA CHAINS, AND ONE EACH OF THE BETA, DELTA, AND GAMMA CHAINS
Source: (synth.) TORPEDO CALIFORNICA (Pacific electric ray) / References: UniProt: P02710
Compound detailsTHE COMPLETE RECEPTOR CONSISTS OF A PENTAMER OF TWO ALPHA CHAINS, AND ONE EACH OF THE BETA, DELTA, ...THE COMPLETE RECEPTOR CONSISTS OF A PENTAMER OF TWO ALPHA CHAINS, AND ONE EACH OF THE BETA, DELTA, AND GAMMA CHAINS. THE PEPTIDE STUDIED HERE REPRESENTS THE SECOND TRANS-MEMBRANE SEGMENT OF THE ALPHA CHAIN OF ACETYLCHOLINE RECEPTOR PROTEIN, ALPHA CHAIN (RESIDUES 267 TO 285)
Has protein modificationY
Sequence detailsAMINO ACIDS NUMERATION IN THE ENTRY DOES NOT INCLUDE THE SIGNAL SEQUENCE. THE C-TERMINAL RESIDUE OF ...AMINO ACIDS NUMERATION IN THE ENTRY DOES NOT INCLUDE THE SIGNAL SEQUENCE. THE C-TERMINAL RESIDUE OF THIS ENTRY, THR267, IS AMIDATED.

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111DQF-COSY
121TOCSY
131NOESY
NMR detailsText: THE STRUCTURE WAS DETERMINED USING 2D-1H-NMR SPECTROSCOPY IN THE MEDIUM WHICH SHOULD BE ADEQUATE FOR THE M2 SEGMENT WITH ITS NON-LIPID SURROUNDING IN THE INTACT NICOTINIC ACTYLCHOLINE RECEPTOR. ...Text: THE STRUCTURE WAS DETERMINED USING 2D-1H-NMR SPECTROSCOPY IN THE MEDIUM WHICH SHOULD BE ADEQUATE FOR THE M2 SEGMENT WITH ITS NON-LIPID SURROUNDING IN THE INTACT NICOTINIC ACTYLCHOLINE RECEPTOR. THE PH GIVEN IN THE EXPERIMENTAL DETAILS IS AN APPROXIMATION ONLY FOR THE MIXTURE OF ORGANIC SOLVENTS USED.

-
Sample preparation

DetailsContents: CDCL3/CD3OH=1/1 WITH 0.1 M LICLO4
Sample conditionsIonic strength: 0.1 M LICLO4 / pH: 4 / Pressure: 1 atm / Temperature: 303 K
Crystal grow
*PLUS
Method: other / Details: NMR

-
NMR measurement

NMR spectrometerType: Varian UNITY / Manufacturer: Varian / Model: UNITY / Field strength: 600 MHz

-
Processing

NMR software
NameVersionDeveloperClassification
FANTOM4R.FRACZKIEWICZ,C.MUMENTHALER,B. VON FREYBERG, T.SCHAUMANN,W.BRAUNrefinement
VNMRVNMRstructure solution
XEASYstructure solution
DYANAstructure solution
MARDIGRASstructure solution
RefinementMethod: distance geometry / Software ordinal: 1
Details: REFINEMENT DETAILS CAN BE FOUND IN THE JRNL CITATION ABOVE. THE NMR STUDY HAS BEEN CONDUCTED USING THE SYNTHETIC PEPTIDE WITH METHIONINE 243 REPLACED BY NORLEUCINE. SUCH AN ISOSTERIC ...Details: REFINEMENT DETAILS CAN BE FOUND IN THE JRNL CITATION ABOVE. THE NMR STUDY HAS BEEN CONDUCTED USING THE SYNTHETIC PEPTIDE WITH METHIONINE 243 REPLACED BY NORLEUCINE. SUCH AN ISOSTERIC REPLACEMENT USUALLY DOES NOT AFFECT THE PEPTIDE CONFORMATION, WHILE SYMPLIFYING THE SYNTHESIS. TO AVOID DIFFICULTIES WHICH MAY ARISE FROM THE PRESENCE OF A NONSTANDARD AMINO ACID RESIDUE AS WELL AS FOR THE PURPOSE OF AGREEMENT BETWEEN THE NATIVE M2 FRAGMENT AND THE CONFORMERS TO BE DEPOSITED, THE NORLEUCINE RESIDUE WAS REPLACED BY METHIONINE.
NMR ensembleConformer selection criteria: LEAST RESTRAINTS VIOLATION / Conformers calculated total number: 300 / 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