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- PDB-2ko2: NOGO66 -

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Basic information

Entry
Database: PDB / ID: 2ko2
TitleNOGO66
ComponentsReticulon-4
KeywordsMEMBRANE PROTEIN / NOGO / peripheral / DPC micelle / myelin inhibitor / Endoplasmic reticulum / Membrane / Phosphoprotein / 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 / positive regulation of artery morphogenesis / cerebral cortex radial glia-guided migration / regulation of nervous system development / negative regulation of neuron projection regeneration / positive regulation of neutrophil migration / endoplasmic reticulum tubular network membrane organization ...cell adhesion involved in sprouting angiogenesis / positive regulation of ERBB3 signaling pathway / endoplasmic reticulum tubular network formation / endoplasmic reticulum tubular network organization / positive regulation of artery morphogenesis / cerebral cortex radial glia-guided migration / regulation of nervous system development / negative regulation of neuron projection regeneration / positive regulation of neutrophil migration / endoplasmic reticulum tubular network membrane organization / Axonal growth inhibition (RHOA activation) / endoplasmic reticulum tubular network membrane / negative regulation of vasculogenesis / : / positive regulation of glial cell differentiation / 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 / negative regulation of axonogenesis / positive regulation of mammary gland epithelial cell proliferation / nuclear pore complex assembly / regulation of sensory perception of pain / protein localization to lysosome / cardiac epithelial to mesenchymal transition / negative regulation of axon extension / leukocyte migration involved in inflammatory response / positive regulation of dopamine secretion / blastocyst formation / endoplasmic reticulum organization / axonal fasciculation / positive regulation of hepatocyte proliferation / 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 / negative regulation of neuron differentiation / regulation of cell migration / cell projection / negative regulation of cell growth / positive regulation of angiogenesis / negative regulation of neuron projection development / cell junction / myelin sheath / nuclear envelope / nervous system development / cellular response to hypoxia / postsynaptic density / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / protein stabilization / neuron projection / cadherin binding / neuronal cell body / glutamatergic synapse / ubiquitin protein ligase binding / protein-containing complex binding / endoplasmic reticulum membrane / endoplasmic reticulum / protein homodimerization activity / protein-containing complex / plasma membrane / cytoplasm
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 speciesMus musculus (house mouse)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsCocco, M.J. / Schulz, J. / Vasudevan, S.V.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2010
Title: Protein folding at the membrane interface, the structure of Nogo-66 requires interactions with a phosphocholine surface.
Authors: Vasudevan, S.V. / Schulz, J. / Zhou, C. / Cocco, M.J.
History
DepositionSep 8, 2009Deposition site: BMRB / Processing site: RCSB
Revision 1.0Apr 21, 2010Provider: 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_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.3May 22, 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)9,1441
Polymers9,1441
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 20structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Reticulon-4 / / Neurite outgrowth inhibitor / Nogo protein


Mass: 9144.463 Da / Num. of mol.: 1 / Fragment: Extracellular domain (UNP residues 1025-1090)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Kiaa0886, Nogo, Rtn4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q99P72

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1232D DQF-COSY
1332D 1H-1H NOESY
1432D 1H-1H TOCSY
1523D 1H-15N NOESY
1623D 1H-13C NOESY
1733D (H)CCH-TOCSY
1833D HN(CA)CB
1933D HN(CO)CA
11033D HNCO
11133D HNHA

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Sample preparation

Details
Solution-IDContentsSolvent system
10.5-1.0 mM NOGO-B, 90% H2O/10% D2O90% H2O/10% D2O
20.5-1.0 mM NOGO-B, 90% H2O/10% D2O90% H2O/10% D2O
30.5-1.0 mM NOGO-B, 90% H2O/10% D2O90% H2O/10% D2O
Sample
UnitsComponentConc. range (mg/ml)Solution-ID
mMNOGO-B-10.5-1.01
mMNOGO-B-20.5-1.02
mMNOGO-B-30.5-1.03
Sample conditionsIonic strength: 0.0 / pH: 4.0 / Pressure: AMBIENT / Temperature: 308 K

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NMR measurement

NMR spectrometerType: VARIAN INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR NIH2.2Schwieters, Kuszewski, Tjandra and Clorestructure solution
ANALYSIS1.0.15CCPNchemical shift assignment
NMRDraw2.2Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxdata analysis
X-PLOR NIH2.2Schwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: XPLOR-NIH WAS USED FOR REFINING THE FOLDED PROTEINS. DIHERAL ANGLE RESTRAINTS AND PRE RESTRAINTS WERE ADDED DURING REFINEMENT.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 20 / Conformers submitted total number: 10

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