[English] 日本語
![](img/lk-miru.gif)
- EMDB-7735: Single-Molecule 3D Image of neurexin 1 alpha by Individual Partic... -
+
Open data
-
Basic information
Entry | Database: EMDB / ID: EMD-7735 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Single-Molecule 3D Image of neurexin 1 alpha by Individual Particle Electron Tomography (No. 077) | |||||||||
![]() | Neurexin 1 alpha | |||||||||
![]() |
| |||||||||
Biological species | ![]() ![]() | |||||||||
Method | electron tomography / negative staining / Resolution: 15.5 Å | |||||||||
![]() | Liu JF / Misra A / Reddy S / White MA / Ren G / Rudenko G | |||||||||
![]() | ![]() 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 |
|
-
Structure visualization
Movie |
![]() |
---|---|
Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
-
Downloads & links
-EMDB archive
Map data | ![]() | 39 MB | ![]() | |
---|---|---|---|---|
Header (meta data) | ![]() ![]() | 10 KB 10 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 7.9 KB | Display | ![]() |
Images | ![]() | 17 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7639C ![]() 7640C ![]() 7641C ![]() 7642C ![]() 7643C ![]() 7644C ![]() 7645C ![]() 7646C ![]() 7647C ![]() 7648C ![]() 7649C ![]() 7650C ![]() 7651C ![]() 7652C ![]() 7653C ![]() 7654C ![]() 7655C ![]() 7656C ![]() 7657C ![]() 7658C ![]() 7659C ![]() 7660C ![]() 7661C ![]() 7662C ![]() 7663C ![]() 7664C ![]() 7665C ![]() 7666C ![]() 7667C ![]() 7668C ![]() 7669C ![]() 7670C ![]() 7671C ![]() 7672C ![]() 7673C ![]() 7674C ![]() 7675C ![]() 7676C ![]() 7677C ![]() 7678C ![]() 7679C ![]() 7680C ![]() 7681C ![]() 7682C ![]() 7683C ![]() 7684C ![]() 7685C ![]() 7686C ![]() 7687C ![]() 7688C ![]() 7689C ![]() 7690C ![]() 7691C ![]() 7692C ![]() 7693C ![]() 7694C ![]() 7695C ![]() 7696C ![]() 7697C ![]() 7698C ![]() 7699C ![]() 7700C ![]() 7701C ![]() 7702C ![]() 7703C ![]() 7704C ![]() 7705C ![]() 7706C ![]() 7707C ![]() 7708C ![]() 7709C ![]() 7710C ![]() 7711C ![]() 7712C ![]() 7713C ![]() 7714C ![]() 7715C ![]() 7716C ![]() 7717C ![]() 7718C ![]() 7719C ![]() 7720C ![]() 7721C ![]() 7722C ![]() 7723C ![]() 7724C ![]() 7725C ![]() 7726C ![]() 7727C ![]() 7728C ![]() 7729C ![]() 7730C ![]() 7731C ![]() 7732C ![]() 7733C ![]() 7734C ![]() 7736C ![]() 7737C ![]() 7738C ![]() 7739C ![]() 7740C ![]() 7741C ![]() 7742C ![]() 7743C ![]() 7744C ![]() 7745C ![]() 7746C ![]() 7747C ![]() 7748C ![]() 7749C ![]() 7750C ![]() 7751C ![]() 7752C ![]() 7753C ![]() 7754C ![]() 7755C ![]() 7756C ![]() 7757C ![]() 7758C ![]() 7759C ![]() 7760C ![]() 7761C ![]() 7762C ![]() 7763C ![]() 7764C ![]() 7765C ![]() 7766C ![]() 7767C ![]() 7768C ![]() 6cw1C C: citing same article ( |
---|---|
Similar structure data |
-
Links
EMDB pages | ![]() ![]() |
---|
-
Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Neurexin 1 alpha | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.48 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-
Sample components
-Entire : neurexin 1 alpha
Entire | Name: neurexin 1 alpha |
---|---|
Components |
|
-Supramolecule #1: neurexin 1 alpha
Supramolecule | Name: neurexin 1 alpha / type: organelle_or_cellular_component / ID: 1 / Parent: 0 |
---|---|
Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 0.137 kDa/nm |
Recombinant expression | Organism: ![]() |
-Experimental details
-Structure determination
Method | negative staining |
---|---|
![]() | electron tomography |
Aggregation state | particle |
-
Sample preparation
Buffer | pH: 8 / Details: 25 mM Tris pH 8, 100 mM NaCl, 3 mM CaCl2 |
---|---|
Staining | Type: NEGATIVE / Material: uranyl formate Details: The grid was stained for 15 s by sequential submersion in two drops of uranyl formate (UF). |
Grid | Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.039 kPa |
Details | The purified neurexin 1 alpha proteins were stored in 25 mM Tris pH 8, 100 mM NaCl in flash-frozen aliquots. |
Sectioning | Other: NO SECTIONING |
-
Electron microscopy
Microscope | ZEISS LIBRA120PLUS |
---|---|
Specialist optics | Energy filter - Name: In-column Omega Filter |
Image recording | Film 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 beam | Acceleration voltage: 120 kV / Electron source: LAB6 |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.2 mm / Nominal magnification: 80000 |