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- EMDB-7665: Single-Molecule 3D Image of neurexin 1 alpha by Individual Partic... -

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Database: EMDB / ID: EMD-7665
TitleSingle-Molecule 3D Image of neurexin 1 alpha by Individual Particle Electron Tomography (No. 007)
Map data
Sampleneurexin 1 alpha
Biological speciesBos taurus (cattle)
Methodelectron tomography / negative staining / Resolution: 16.27 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.
DepositionMar 27, 2018-
Header (metadata) releaseAug 1, 2018-
Map releaseSep 19, 2018-
UpdateJan 22, 2020-
Current statusJan 22, 2020Processing site: RCSB / Status: Released

Structure visualization

  • Surface view with section colored by density value
  • Surface level: 0.5
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.5
  • Imaged by UCSF Chimera
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Structure viewerEM map:
Supplemental images

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FileDownload / File: emd_7665.map.gz / Format: CCP4 / Size: 42.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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



Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.48 Å
Contour LevelMovie #1: 0.5
Minimum - Maximum-0.2833674 - 3.5133498
Average (Standard dev.)0.018424189 (±0.1435841)
SymmetrySpace group: 1


Map geometry
Axis orderXYZ
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
MAP C/R/S123
start NC/NR/NS-112-112-112
D min/max/mean-0.2833.5130.018

Supplemental data

Sample components

Entire neurexin 1 alpha

EntireName: neurexin 1 alpha / Number of components: 1

Component #1: cellular-component, neurexin 1 alpha

Cellular-componentName: neurexin 1 alpha / Recombinant expression: No
MassTheoretical: 137 kDa
SourceSpecies: Bos taurus (cattle)
Source (engineered)Expression System: unidentified baculovirus

Experimental details

Sample preparation

SpecimenSpecimen state: Particle / Method: negative staining
Sample solutionBuffer solution: 25 mM Tris pH 8, 100 mM NaCl, 3 mM CaCl2 / pH: 8
StainingThe grid was stained for 15 s by sequential submersion in two drops of uranyl formate (UF).
VitrificationCryogen name: NONE

Electron microscopy imaging

ImagingMicroscope: ZEISS LIBRA120PLUS
Electron gunElectron source: LAB6 / Accelerating voltage: 120 kV / Electron dose: 15 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 80000.0 X (nominal) / Cs: 2.2 mm / Imaging mode: BRIGHT FIELD / Energy filter: In-column Omega Filter
Specimen HolderModel: OTHER
CameraDetector: GATAN ULTRASCAN 4000 (4k x 4k)

Image acquisition

Image acquisitionNumber of digital images: 81

Image processing

ProcessingMethod: electron tomography / Number of sections: 65
Details: X-ray speckles in images were removed before alignment and 3D reconstruction.
3D reconstructionAlgorithm: FOURIER SPACE
CTF correction: Micrographs were aligned together by IMOD. The CTF was corrected by TOMOCTF.
Resolution: 16.27 Å / Resolution method: FSC 0.5 CUT-OFF
Details: The 3D reconstruction was performed by Individual-Particle Electron Tomography (IPET).
FSC plot (resolution estimation)

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