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- PDB-8g21: Reelin C-Terminal Region -

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Basic information

Entry
Database: PDB / ID: 8g21
TitleReelin C-Terminal Region
ComponentsReelin
KeywordsSUGAR BINDING PROTEIN / Alzheimers disease / GAG interaction
Function / homology
Function and homology information


: / spinal cord patterning / cerebral cortex tangential migration / reelin complex / positive regulation of lateral motor column neuron migration / lateral motor column neuron migration / lipoprotein particle receptor binding / regulation of synaptic activity / interneuron migration / postsynaptic density protein 95 clustering ...: / spinal cord patterning / cerebral cortex tangential migration / reelin complex / positive regulation of lateral motor column neuron migration / lateral motor column neuron migration / lipoprotein particle receptor binding / regulation of synaptic activity / interneuron migration / postsynaptic density protein 95 clustering / : / positive regulation of CREB transcription factor activity / ventral spinal cord development / Reelin signalling pathway / reelin-mediated signaling pathway / regulation of behavior / positive regulation of synapse maturation / regulation of neuron migration / layer formation in cerebral cortex / glial cell differentiation / receptor localization to synapse / positive regulation of dendritic spine morphogenesis / protein localization to synapse / NMDA glutamate receptor clustering / very-low-density lipoprotein particle receptor binding / positive regulation of small GTPase mediated signal transduction / regulation of NMDA receptor activity / positive regulation of AMPA receptor activity / regulation of neuron differentiation / response to pain / dendrite development / associative learning / positive regulation of excitatory postsynaptic potential / positive regulation of protein tyrosine kinase activity / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / positive regulation of TOR signaling / positive regulation of protein kinase activity / long-term memory / serine-type peptidase activity / positive regulation of synaptic transmission, glutamatergic / extracellular matrix / positive regulation of long-term synaptic potentiation / locomotory behavior / central nervous system development / hippocampus development / long-term synaptic potentiation / axon guidance / neuron migration / modulation of chemical synaptic transmission / brain development / positive regulation of neuron projection development / peptidyl-tyrosine phosphorylation / positive regulation of peptidyl-tyrosine phosphorylation / cell adhesion / positive regulation of protein phosphorylation / dendrite / proteolysis / extracellular space / extracellular region / metal ion binding / plasma membrane / cytoplasm
Similarity search - Function
Reelin / Reeler domain / Reeler domain / Reeler domain superfamily / Reelin domain profile. / Tenascin, EGF-like domain / Tenascin EGF domain / Sialidase superfamily / Epidermal growth factor-like domain. / EGF-like domain profile. ...Reelin / Reeler domain / Reeler domain / Reeler domain superfamily / Reelin domain profile. / Tenascin, EGF-like domain / Tenascin EGF domain / Sialidase superfamily / Epidermal growth factor-like domain. / EGF-like domain profile. / EGF-like domain signature 2. / EGF-like domain signature 1. / EGF-like domain
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / na
AuthorsChandrahas, A.S. / Marino, C. / Arboleda-Velasquez, J.F.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)UH3 NS100121 United States
National Institutes of Health/National Institute on Aging (NIH/NIA)RF1 NS110048 United States
CitationJournal: Nat Med / Year: 2023
Title: Resilience to autosomal dominant Alzheimer's disease in a Reelin-COLBOS heterozygous man.
Authors: Lopera, F. / Marino, C. / Chandrahas, A.S. / O'Hare, M. / Villalba-Moreno, N.D. / Aguillon, D. / Baena, A. / Sanchez, J.S. / Vila-Castelar, C. / Ramirez Gomez, L. / Chmielewska, N. / ...Authors: Lopera, F. / Marino, C. / Chandrahas, A.S. / O'Hare, M. / Villalba-Moreno, N.D. / Aguillon, D. / Baena, A. / Sanchez, J.S. / Vila-Castelar, C. / Ramirez Gomez, L. / Chmielewska, N. / Oliveira, G.M. / Littau, J.L. / Hartmann, K. / Park, K. / Krasemann, S. / Glatzel, M. / Schoemaker, D. / Gonzalez-Buendia, L. / Delgado-Tirado, S. / Arevalo-Alquichire, S. / Saez-Torres, K.L. / Amarnani, D. / Kim, L.A. / Mazzarino, R.C. / Gordon, H. / Bocanegra, Y. / Villegas, A. / Gai, X. / Bootwalla, M. / Ji, J. / Shen, L. / Kosik, K.S. / Su, Y. / Chen, Y. / Schultz, A. / Sperling, R.A. / Johnson, K. / Reiman, E.M. / Sepulveda-Falla, D. / Arboleda-Velasquez, J.F. / Quiroz, Y.T.
History
DepositionFeb 3, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 31, 2023Provider: repository / Type: Initial release
Revision 1.1Jun 7, 2023Group: Database references / Structure summary / Category: audit_author / citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Reelin


Theoretical massNumber of molelcules
Total (without water)4,2261
Polymers4,2261
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 / 20structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein/peptide Reelin


Mass: 4225.879 Da / Num. of mol.: 1 / Fragment: C-terminal residues 3429-3460
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RELN / Production host: Escherichia coli (E. coli)
References: UniProt: P78509, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic11H TOCSY
121isotropic11H NOESY
131isotropic12D 1H-15N
141isotropic12D 1H-13C

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Sample preparation

DetailsType: solution
Contents: 3.3 mM [U-98% 15N] Reelin CTR, 50 % v/v THF (CF3-CD2-OH), 0.25 mM DSS (4,4-dimethyl-4-silapentane-1-sulfonic acid), 50% H2O/50% D2O
Details: 50% (V/V) H2O, 50% (V/V) THF (CF3-CD2-OH), 0.25 mM DSS (4,4-dimethyl-4-silapentane-1-sulfonic acid), ~3.3 mM reelin peptide
Label: Reelin CTR / Solvent system: 50% H2O/50% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
3.3 mMReelin CTR[U-98% 15N]1
50 % v/vTHF (CF3-CD2-OH)natural abundance1
0.25 mMDSS (4,4-dimethyl-4-silapentane-1-sulfonic acid)natural abundance1
Sample conditionsIonic strength units: Not defined / Label: standard conditions / pH: 7.4 / Pressure units: Pa / Temperature: 298.15 K

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NMR measurement

NMR spectrometerType: Agilent Direct Drive / Manufacturer: Agilent / Model: Direct Drive / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CNS1.2.1Brunger A. T. et.al.refinement
ARIA2.3.2Linge, O'Donoghue and Nilgesstructure calculation
PSVSBhattacharya and Montelionedata analysis
CcpNmr Analysis2.4.2CCPNdata analysis
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxdata analysis
PyMOL2.5.4Schrodinger and DeLanodata analysis
CNS1.2.1Brunger A. T. et.al.structure calculation
RefinementMethod: na / Software ordinal: 1
Details: 20 best structures superimposed on backbone atoms (N,CA,C,O)
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 20 / Conformers submitted total number: 20

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