[English] 日本語
Yorodumi
- PDB-2jv5: Nogo54 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2jv5
TitleNogo54
ComponentsReticulon-4
KeywordsPROTEIN BINDING / Nogo54 / Alternative splicing / Endoplasmic reticulum / Membrane / Phosphorylation / Transmembrane
Function / homology
Function and homology information


cell adhesion involved in sprouting angiogenesis / positive regulation of ERBB3 signaling pathway / negative regulation of vasculogenesis / endoplasmic reticulum tubular network formation / positive regulation of neutrophil migration / cerebral cortex radial glia-guided migration / cell migration involved in vasculogenesis / endoplasmic reticulum tubular network organization / endoplasmic reticulum tubular network membrane / endoplasmic reticulum tubular network membrane organization ...cell adhesion involved in sprouting angiogenesis / positive regulation of ERBB3 signaling pathway / negative regulation of vasculogenesis / endoplasmic reticulum tubular network formation / positive regulation of neutrophil migration / cerebral cortex radial glia-guided migration / cell migration involved in vasculogenesis / endoplasmic reticulum tubular network organization / endoplasmic reticulum tubular network membrane / endoplasmic reticulum tubular network membrane organization / positive regulation of macrophage migration / positive regulation of artery morphogenesis / positive regulation of protein localization to endoplasmic reticulum / intracellular sphingolipid homeostasis / endoplasmic reticulum tubular network / central nervous system vasculogenesis / regulation of branching morphogenesis of a nerve / positive regulation of toll-like receptor 9 signaling pathway / positive regulation of mammary gland epithelial cell proliferation / nuclear pore complex assembly / negative regulation of axon extension / cardiac epithelial to mesenchymal transition / protein localization to lysosome / Axonal growth inhibition (RHOA activation) / leukocyte migration involved in inflammatory response / positive regulation of hepatocyte proliferation / blastocyst formation / endoplasmic reticulum organization / axonal fasciculation / anchoring junction / positive regulation of macrophage cytokine production / negative regulation of amyloid-beta formation / positive regulation of Rac protein signal transduction / positive regulation of epithelial cell migration / regulation of postsynapse assembly / regulation of cell migration / negative regulation of cell growth / brain development / modulation of chemical synaptic transmission / neuron differentiation / positive regulation of angiogenesis / cell junction / nuclear envelope / regulation of apoptotic process / cellular response to hypoxia / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / neuron projection / postsynaptic density / protein stabilization / cadherin binding / neuronal cell body / apoptotic process / synapse / ubiquitin protein ligase binding / endoplasmic reticulum membrane / glutamatergic synapse / endoplasmic reticulum / protein homodimerization activity / RNA binding / metal ion binding / plasma membrane
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2480 / Reticulon / : / Reticulon / Reticulon domain profile. / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / distance geometry
AuthorsLi, M. / Song, J.
CitationJournal: To be Published
Title: Structure-based design of buffer-soluble Nogo54: a molecular mimic of Nogo-66 to inhibit CNS neuron regeneration
Authors: Li, M. / Song, J.
History
DepositionSep 12, 2007Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Sep 16, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_spectrometer ...database_2 / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_spectrometer.model
Revision 1.3May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Reticulon-4


Theoretical massNumber of molelcules
Total (without water)6,1861
Polymers6,1861
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 / 200target function
RepresentativeModel #1closest to the average

-
Components

#1: Protein Reticulon-4 / Neurite outgrowth inhibitor / Nogo protein / Foocen / Neuroendocrine-specific protein / NSP / ...Neurite outgrowth inhibitor / Nogo protein / Foocen / Neuroendocrine-specific protein / NSP / Neuroendocrine-specific protein C homolog / RTN-x / Reticulon-5


Mass: 6186.020 Da / Num. of mol.: 1 / Fragment: UNP residues 1055-1108
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RTN4, KIAA0886, NOGO / Plasmid: pet32a / Production host: Escherichia coli (E. coli) / References: UniProt: Q9NQC3

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D 1H-15N NOESY
1313D 1H-15N TOCSY

-
Sample preparation

DetailsContents: 0.1mM [U-100% 15N] nogo protein; 90% H2O, 10% D2O / Solvent system: 90% H2O/10% D2O
SampleConc.: 0.1 mM / Component: nogo protein / Isotopic labeling: [U-100% 15N]
Sample conditionsIonic strength: 10 / pH: 4.5 / Pressure: ambient / Temperature: 273 K

-
NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz

-
Processing

NMR softwareName: CYANA / Developer: Guntert, Mumenthaler and Wuthrich / Classification: refinement
RefinementMethod: distance geometry / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 200 / 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