[English] 日本語
Yorodumi
- PDB-2ncm: NEURAL CELL ADHESION MOLECULE, NMR, 20 STRUCTURES -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2ncm
TitleNEURAL CELL ADHESION MOLECULE, NMR, 20 STRUCTURES
ComponentsNEURAL CELL ADHESION MOLECULE
KeywordsCELL ADHESION / GLYCOPROTEIN / HEPARIN-BINDING / GPI-ANCHOR / NEURAL ADHESION MOLECULE / IMMUNOGLOBULIN FOLD
Function / homology
Function and homology information


regulation of exocyst assembly / NCAM1 interactions / Signal transduction by L1 / regulation of semaphorin-plexin signaling pathway / NCAM signaling for neurite out-growth / LRR domain binding / homotypic cell-cell adhesion / RAF/MAP kinase cascade / thalamus development / commissural neuron axon guidance ...regulation of exocyst assembly / NCAM1 interactions / Signal transduction by L1 / regulation of semaphorin-plexin signaling pathway / NCAM signaling for neurite out-growth / LRR domain binding / homotypic cell-cell adhesion / RAF/MAP kinase cascade / thalamus development / commissural neuron axon guidance / axonal fasciculation / negative regulation of programmed cell death / epithelial to mesenchymal transition / neuron development / multicellular organismal response to stress / phosphatase binding / positive regulation of cardiac muscle cell proliferation / positive regulation of calcium-mediated signaling / response to cocaine / response to lead ion / calcium-mediated signaling / modulation of chemical synaptic transmission / Schaffer collateral - CA1 synapse / neuron projection development / cell-cell junction / myelin sheath / heparin binding / presynaptic membrane / growth cone / postsynaptic membrane / learning or memory / cell surface receptor signaling pathway / response to xenobiotic stimulus / axon / external side of plasma membrane / neuronal cell body / glutamatergic synapse / plasma membrane
Similarity search - Function
Neural cell adhesion / : / Immunoglobulin domain / Immunoglobulin I-set / Immunoglobulin I-set domain / Fibronectin type III domain / Fibronectin type 3 domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin V-Type ...Neural cell adhesion / : / Immunoglobulin domain / Immunoglobulin I-set / Immunoglobulin I-set domain / Fibronectin type III domain / Fibronectin type 3 domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin V-Type / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Neural cell adhesion molecule 1 / Neural cell adhesion molecule 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR
AuthorsThomsen, N.K. / Poulsen, F.M.
CitationJournal: Nat.Struct.Biol. / Year: 1996
Title: The three-dimensional structure of the first domain of neural cell adhesion molecule.
Authors: Thomsen, N.K. / Soroka, V. / Jensen, P.H. / Berezin, V. / Kiselyov, V.V. / Bock, E. / Poulsen, F.M.
History
DepositionDec 16, 1996Processing site: BNL
SupersessionMar 12, 1997ID: 1NCM
Revision 1.0Mar 12, 1997Provider: 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 1.4Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: NEURAL CELL ADHESION MOLECULE


Theoretical massNumber of molelcules
Total (without water)10,8641
Polymers10,8641
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / -
Representative

-
Components

#1: Protein NEURAL CELL ADHESION MOLECULE / NCAM DOMAIN 1


Mass: 10863.947 Da / Num. of mol.: 1 / Fragment: DOMAIN 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Strain: C57BL/6 / Organ: BRAIN / Plasmid: PHIL-S1 / Production host: Pichia pastoris (fungus) / References: UniProt: P13594, UniProt: P13595*PLUS
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR

-
Sample preparation

Crystal grow
*PLUS
Method: other / Details: NMR

-
Processing

NMR ensembleConformers 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