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- EMDB-23091: Reelin central fragment repeats 3-6, dimer -

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Basic information

Entry
Database: EMDB / ID: EMD-23091
TitleReelin central fragment repeats 3-6, dimer
Map dataSubtomogram average for Reelin repeat 3-6 dimer
Sample
  • Complex: Reelin central fragment, repeat 3-6 dimer
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 / Reelin signalling pathway / 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 / Reelin signalling pathway / lipoprotein particle receptor binding / regulation of synaptic activity / interneuron migration / postsynaptic density protein 95 clustering / positive regulation of CREB transcription factor activity / postsynaptic density assembly / ventral spinal cord development / reelin-mediated signaling pathway / regulation of behavior / positive regulation of synapse maturation / motor neuron migration / 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 / dentate gyrus development / 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 / long-term memory / forebrain development / serine-type peptidase activity / positive regulation of synaptic transmission, glutamatergic / extracellular matrix / learning / 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 / cell morphogenesis / brain development / cerebral cortex development / positive regulation of neuron projection development / positive regulation of peptidyl-tyrosine phosphorylation / cell migration / regulation of gene expression / perikaryon / collagen-containing extracellular matrix / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / cell adhesion / neuron projection / positive regulation of protein phosphorylation / axon / neuronal cell body / dendrite / proteolysis / extracellular space / metal ion binding / plasma membrane / cytoplasm
Similarity search - Function
: / Reelin subrepeat B / Reelin / Reeler domain / Reeler domain superfamily / Reelin domain profile. / Tenascin, EGF-like domain / Tenascin EGF domain / Sialidase superfamily / Epidermal growth factor-like domain. ...: / Reelin subrepeat B / Reelin / 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 speciesMus musculus (house mouse)
Methodsubtomogram averaging / cryo EM / Resolution: 20.0 Å
AuthorsDai W / Chen M / Kuang X / Huynh K / D'Arcangelo G / Turk LS / Comoletti D
Funding support United States, 3 items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)1755189 United States
National Science Foundation (NSF, United States)1755184 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM008339 United States
CitationJournal: Structure / Year: 2021
Title: The structure-function relationship of a signaling-competent, dimeric Reelin fragment.
Authors: Liam S Turk / Xuyuan Kuang / Valentina Dal Pozzo / Khush Patel / Muyuan Chen / Kevin Huynh / Michael J Currie / Daniel Mitchell / Renwick C J Dobson / Gabriella D'Arcangelo / Wei Dai / Davide Comoletti /
Abstract: Reelin operates through canonical and non-canonical pathways that mediate several aspects of brain development and function. Reelin's dimeric central fragment (CF), generated through proteolytic ...Reelin operates through canonical and non-canonical pathways that mediate several aspects of brain development and function. Reelin's dimeric central fragment (CF), generated through proteolytic cleavage, is required for the lipoprotein-receptor-dependent canonical pathway activation. Here, we analyze the signaling properties of a variety of Reelin fragments and measure the differential binding affinities of monomeric and dimeric CF fragments to lipoprotein receptors to investigate the mode of canonical signal activation. We also present the cryoelectron tomography-solved dimeric structure of Reelin CF and support it using several other biophysical techniques. Our findings suggest that Reelin CF forms a covalent parallel dimer with some degree of flexibility between the two protein chains. As a result of this conformation, Reelin binds to lipoprotein receptors in a manner inaccessible to its monomeric form and is capable of stimulating canonical pathway signaling.
History
DepositionDec 10, 2020-
Header (metadata) releaseJun 2, 2021-
Map releaseJun 2, 2021-
UpdateOct 20, 2021-
Current statusOct 20, 2021Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 6.8
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 6.8
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_23091.png

Downloads & links

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Map

FileDownload / File: emd_23091.map.gz / Format: CCP4 / Size: 2.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSubtomogram average for Reelin repeat 3-6 dimer
Voxel sizeX=Y=Z: 5.56 Å
Density
Contour LevelBy AUTHOR: 6.8 / Movie #1: 6.8
Minimum - Maximum-13.917358 - 25.612045
Average (Standard dev.)0.020357516 (±0.99862045)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions848484
Spacing848484
CellA=B=C: 467.04 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z5.565.565.56
M x/y/z848484
origin x/y/z0.0000.0000.000
length x/y/z467.040467.040467.040
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ256256256
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS848484
D min/max/mean-13.91725.6120.020

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Supplemental data

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Sample components

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Entire : Reelin central fragment, repeat 3-6 dimer

EntireName: Reelin central fragment, repeat 3-6 dimer
Components
  • Complex: Reelin central fragment, repeat 3-6 dimer

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Supramolecule #1: Reelin central fragment, repeat 3-6 dimer

SupramoleculeName: Reelin central fragment, repeat 3-6 dimer / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Mus musculus (house mouse)
Recombinant expressionOrganism: Homo sapiens (human)

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation stateparticle

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Sample preparation

Concentration0.1 mg/mL
BufferpH: 7.4
GridModel: Quantifoil / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 298 K / Instrument: LEICA EM GP

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Specialist opticsPhase plate: VOLTA PHASE PLATE / Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 1.5 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus min: 4.0 µm / Nominal magnification: 39000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 20.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number subtomograms used: 800
ExtractionNumber tomograms: 50 / Number images used: 9000 / Software - Name: EMAN2
Final angle assignmentType: NOT APPLICABLE

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