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- EMDB-7708: Single-Molecule 3D Image of neurexin 1 alpha by Individual Partic... -

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Basic information

Entry
Database: EMDB / ID: EMD-7708
TitleSingle-Molecule 3D Image of neurexin 1 alpha by Individual Particle Electron Tomography (No. 051)
Map dataneurexin 1 alpha
Sample
  • Organelle or cellular component: neurexin 1 alpha
Biological speciesBos taurus (cattle)
Methodelectron tomography / negative staining / Resolution: 15.6 Å
AuthorsLiu JF / Misra A / Reddy S / White MA / Ren G / Rudenko G
Funding support United States, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Mental Health (NIH/NIMH)R01MH077303 United States
Department of Energy (DOE, United States)DE-AC02-05CH11231 United States
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)R01HL115153 United States
CitationJournal: J Mol Biol / Year: 2018
Title: Structural Plasticity of Neurexin 1α: Implications for its Role as Synaptic Organizer.
Authors: Jianfang Liu / Anurag Misra / M V V V Sekhar Reddy / Mark Andrew White / Gang Ren / Gabby Rudenko /
Abstract: α-Neurexins are synaptic organizing molecules implicated in neuropsychiatric disorders. They bind and arrange an array of different partners in the synaptic cleft. The extracellular region of ...α-Neurexins are synaptic organizing molecules implicated in neuropsychiatric disorders. They bind and arrange an array of different partners in the synaptic cleft. The extracellular region of neurexin 1α (n1α) contains six LNS domains (L1-L6) interspersed by three Egf-like repeats. N1α must encode highly evolved structure-function relationships in order to fit into the narrow confines of the synaptic cleft, and also recruit its large, membrane-bound partners. Internal molecular flexibility could provide a solution; however, it is challenging to delineate because currently no structural methods permit high-resolution structure determination of large, flexible, multi-domain protein molecules. To investigate the structural plasticity of n1α, in particular the conformation of domains that carry validated binding sites for different protein partners, we used a panel of structural techniques. Individual particle electron tomography revealed that the N-terminally and C-terminally tethered domains, L1 and L6, have a surprisingly limited range of conformational freedom with respect to the linear central core containing L2 through L5. A 2.8-Å crystal structure revealed an unexpected arrangement of the L2 and L3 domains. Small-angle X-ray scattering and electron tomography indicated that incorporation of the alternative splice insert SS6 relieves the restricted conformational freedom between L5 and L6, suggesting that SS6 may work as a molecular toggle. The architecture of n1α thus encodes a combination of rigid and flexibly tethered domains that are uniquely poised to work together to promote its organizing function in the synaptic cleft, and may permit allosterically regulated and/or concerted protein partner binding.
History
DepositionMar 27, 2018-
Header (metadata) releaseMay 2, 2018-
Map releaseSep 19, 2018-
UpdateJan 22, 2020-
Current statusJan 22, 2020Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.5
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.5
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_7708.png

Downloads & links

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Map

FileDownload / File: emd_7708.map.gz / Format: CCP4 / Size: 42.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationneurexin 1 alpha
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.48 Å/pix.
x 224 pix.
= 331.52 Å		1.48 Å/pix.
x 224 pix.
= 331.52 Å		1.48 Å/pix.
x 224 pix.
= 331.52 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.48 Å
Density

Histogram

Histogram (log scale)
Contour LevelMovie #1: 0.5
Minimum - Maximum-0.220128 - 3.7510571
Average (Standard dev.)0.01792334 (±0.13891828)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-112-112-112
Dimensions224224224
Spacing224224224
CellA=B=C: 331.52002 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.481.481.48
M x/y/z224224224
origin x/y/z0.0000.0000.000
length x/y/z331.520331.520331.520
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-112-112-112
NC/NR/NS224224224
D min/max/mean-0.2203.7510.018

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Supplemental data

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Sample components

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Entire : neurexin 1 alpha

EntireName: neurexin 1 alpha
Components
  • Organelle or cellular component: neurexin 1 alpha

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Supramolecule #1: neurexin 1 alpha

SupramoleculeName: neurexin 1 alpha / type: organelle_or_cellular_component / ID: 1 / Parent: 0
Source (natural)Organism: Bos taurus (cattle)
Molecular weightTheoretical: 137 MDa
Recombinant expressionOrganism: unidentified baculovirus

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Experimental details

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Structure determination

Methodnegative staining
Processingelectron tomography
Aggregation stateparticle

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Sample preparation

BufferpH: 8 / Details: 25 mM Tris pH 8, 100 mM NaCl, 3 mM CaCl2
StainingType: NEGATIVE / Material: uranyl formate
Details: The grid was stained for 15 s by sequential submersion in two drops of uranyl formate (UF).
GridMaterial: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.039 kPa
DetailsThe purified neurexin 1 alpha proteins were stored in 25 mM Tris pH 8, 100 mM NaCl in flash-frozen aliquots.
SectioningOther: NO SECTIONING

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Electron microscopy

MicroscopeZEISS LIBRA120PLUS
Specialist opticsEnergy filter - Name: In-column Omega Filter
Image recordingFilm or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number real images: 81 / Average exposure time: 1.0 sec. / Average electron dose: 15.0 e/Å2
Electron beamAcceleration voltage: 120 kV / Electron source: LAB6
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.2 mm / Nominal magnification: 80000

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Image processing

DetailsX-ray speckles in images were removed before alignment and 3D reconstruction.
Final reconstructionAlgorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 15.6 Å / Resolution method: FSC 0.5 CUT-OFF
Details: The 3D reconstruction was performed by Individual-Particle Electron Tomography (IPET).
Number images used: 65
CTF correctionSoftware: (Name: TOMOCTF, IMOD)
Details: Micrographs were aligned together by IMOD. The CTF was corrected by TOMOCTF.
FSC plot (resolution estimation)

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