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- PDB-2jv5: Nogo54 -

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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 / endoplasmic reticulum tubular network formation / endoplasmic reticulum tubular network organization / cerebral cortex radial glia-guided migration / positive regulation of neutrophil migration / endoplasmic reticulum tubular network membrane organization / endoplasmic reticulum tubular network membrane / negative regulation of vasculogenesis / positive regulation of artery morphogenesis ...cell adhesion involved in sprouting angiogenesis / positive regulation of ERBB3 signaling pathway / endoplasmic reticulum tubular network formation / endoplasmic reticulum tubular network organization / cerebral cortex radial glia-guided migration / positive regulation of neutrophil migration / endoplasmic reticulum tubular network membrane organization / endoplasmic reticulum tubular network membrane / negative regulation of vasculogenesis / positive regulation of artery morphogenesis / positive regulation of macrophage migration / cell migration involved in vasculogenesis / positive regulation of protein localization to endoplasmic reticulum / intracellular sphingolipid homeostasis / endoplasmic reticulum tubular network / regulation of branching morphogenesis of a nerve / central nervous system vasculogenesis / positive regulation of toll-like receptor 9 signaling pathway / positive regulation of mammary gland epithelial cell proliferation / nuclear pore complex assembly / protein localization to lysosome / cardiac epithelial to mesenchymal transition / negative regulation of axon extension / leukocyte migration involved in inflammatory response / Axonal growth inhibition (RHOA activation) / blastocyst formation / endoplasmic reticulum organization / axonal fasciculation / positive regulation of hepatocyte proliferation / anchoring junction / positive regulation of macrophage cytokine production / positive regulation of epithelial cell migration / positive regulation of Rac protein signal transduction / negative regulation of amyloid-beta formation / regulation of cell migration / modulation of chemical synaptic transmission / neuron differentiation / brain development / negative regulation of cell growth / positive regulation of angiogenesis / cell junction / nuclear envelope / cellular response to hypoxia / regulation of apoptotic process / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / postsynaptic density / protein stabilization / cadherin binding / neuron projection / glutamatergic synapse / apoptotic process / synapse / ubiquitin protein ligase binding / endoplasmic reticulum membrane / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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

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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

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Experimental details

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Experiment

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

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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

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NMR measurement

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

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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

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