|Entry||Database: EMDB / ID: 7761|
|Title||Single-Molecule 3D Image of neurexin 1 alpha by Individual Particle Electron Tomography (No. 103)|
|Map data||Single-Molecule 3D Image of neurexin 1 alpha by Individual Particle Electron Tomography (No. 103)|
|Sample||neurexin 1 alpha:|
|Source||Bos taurus (cattle)|
|Method||electron tomography / negative staining / 15.2 Å resolution|
|Authors||Liu JF / Misra A / Reddy S / White MA / Ren G / Rudenko G|
|Citation||Journal: 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.
|Date||Deposition: Mar 28, 2018 / Header (metadata) release: Apr 18, 2018 / Map release: Sep 19, 2018 / Last update: Oct 24, 2018|
|Structure viewer||EM map: |
Downloads & links
|File||emd_7761.map.gz (map file in CCP4 format, 44958 KB)|
|Projections & slices|
Images are generated by Spider.
|Voxel size||X=Y=Z: 1.48 Å|
CCP4 map header:
-Entire neurexin 1 alpha
|Entire||Name: neurexin 1 alpha / Number of components: 1|
-Component #1: cellular-component, neurexin 1 alpha
|Cellular-component||Name: neurexin 1 alpha / Recombinant expression: No|
|Mass||Theoretical: 137 kDa|
|Source||Species: Bos taurus (cattle)|
|Source (engineered)||Expression System: unidentified baculovirus|
|Specimen||Specimen state: particle / Method: negative staining|
|Sample solution||Buffer solution: 25 mM Tris pH 8, 100 mM NaCl, 3 mM CaCl2 / pH: 8|
|Staining||The grid was stained for 15 s by sequential submersion in two drops of uranyl formate (UF).|
|Vitrification||Cryogen name: NONE|
-Electron microscopy imaging
|Imaging||Microscope: ZEISS LIBRA120PLUS|
|Electron gun||Electron source: LAB6 / Accelerating voltage: 120 kV / Electron dose: 15 e/Å2 / Illumination mode: FLOOD BEAM|
|Lens||Magnification: 80000.0 X (nominal) / Cs: 2.2 mm / Imaging mode: BRIGHT FIELD / Energy filter: In-column Omega Filter|
|Specimen Holder||Model: OTHER|
|Camera||Detector: GATAN ULTRASCAN 4000 (4k x 4k)|
|Image acquisition||Number of digital images: 81|
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