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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 / positive regulation of AMPA receptor activity / regulation of synaptic activity / interneuron migration ...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 / positive regulation of AMPA receptor activity / regulation of synaptic activity / interneuron migration / positive regulation of CREB transcription factor activity / postsynaptic density protein 95 clustering / postsynaptic density assembly / regulation of behavior / ventral spinal cord development / positive regulation of synapse maturation / layer formation in cerebral cortex / motor neuron migration / receptor localization to synapse / NMDA glutamate receptor clustering / glial cell differentiation / regulation of neuron migration / positive regulation of dendritic spine morphogenesis / protein localization to synapse / reelin-mediated signaling pathway / very-low-density lipoprotein particle receptor binding / regulation of synapse maturation / regulation of NMDA receptor activity / positive regulation of small GTPase mediated signal transduction / regulation of neuron differentiation / response to pain / positive regulation of protein tyrosine kinase activity / associative learning / dendrite development / positive regulation of excitatory postsynaptic potential / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / positive regulation of TOR signaling / long-term memory / forebrain development / serine-type peptidase activity / extracellular matrix / positive regulation of synaptic transmission, glutamatergic / axon guidance / hippocampus development / central nervous system development / learning / positive regulation of long-term synaptic potentiation / locomotory behavior / modulation of chemical synaptic transmission / brain development / cell morphogenesis / cerebral cortex development / positive regulation of neuron projection development / long-term synaptic potentiation / neuron migration / cell migration / regulation of gene expression / : / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / cell adhesion / receptor ligand activity / dendrite / proteolysis / extracellular space / metal ion binding / plasma membrane / cytoplasm
Similarity search - Function
Reelin / : / Reelin subrepeat B / Reeler domain / Reeler domain superfamily / Reelin domain profile. / Teneurin-like EGF domain / Sialidase superfamily / Epidermal growth factor-like domain. / EGF-like domain profile. ...Reelin / : / Reelin subrepeat B / Reeler domain / Reeler domain superfamily / Reelin domain profile. / Teneurin-like EGF domain / Sialidase superfamily / Epidermal growth factor-like domain. / EGF-like domain profile. / EGF-like domain signature 1. / EGF-like domain signature 2. / 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
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
5.56 Å/pix.
x 84 pix.
= 467.04 Å		5.56 Å/pix.
x 84 pix.
= 467.04 Å		5.56 Å/pix.
x 84 pix.
= 467.04 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 5.56 Å
Density

Histogram

Histogram (log scale)
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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