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- PDB-2g31: Human Nogo-A functional domain: nogo60 -

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Basic information

Entry
Database: PDB / ID: 2g31
TitleHuman Nogo-A functional domain: nogo60
ComponentsReticulon-4
KeywordsSIGNALING PROTEIN / NOGO / HELIX
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.F. / Liu, J.X. / Song, J.X.
CitationJournal: Protein Sci. / Year: 2006
Title: Nogo goes in the pure water: solution structure of Nogo-60 and design of the structured and buffer-soluble Nogo-54 for enhancing CNS regeneration
Authors: Li, M.F. / Liu, J.X. / Song, J.X.
History
DepositionFeb 17, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 22, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4May 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)6,8891
Polymers6,8891
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 / Nogo_A / Neurite outgrowth inhibitor / Nogo protein / Foocen / Neuroendocrine-specific protein / ...Nogo_A / Neurite outgrowth inhibitor / Nogo protein / Foocen / Neuroendocrine-specific protein / NSP / Neuroendocrine-specific protein C homolog / RTN-x / Reticulon-5


Mass: 6888.815 Da / Num. of mol.: 1 / Fragment: C_terminal domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Tissue: BRAIN / Gene: NOGO / Plasmid: PET32A / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q9NQC3

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1212D NOESY
1312D TOCSY

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Sample preparation

DetailsContents: 90% H2O, 10% D2O / Solvent system: 90% H2O/10% D2O
Sample conditionspH: 4.0 / Pressure: ambient / Temperature: 278 K

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NMR measurement

NMR spectrometerType: Bruker INOVA / Manufacturer: Bruker / Model: INOVA / Field strength: 800 MHz

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Processing

NMR softwareName: DYANA / Version: CYANA 1.0.6 / Developer: Peter Guntert / 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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