+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-10491 | |||||||||
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Title | Structure of the vertebrate gamma-Tubulin Ring Complex | |||||||||
Map data | Cryo-EM single particle analysis reconstruction of the vertebrate gamma-Tubulin Ring Complex | |||||||||
Sample |
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Function / homology | Function and homology information mitotic spindle microtubule / polar microtubule / gamma-tubulin complex / dense body / microtubule nucleation / gamma-tubulin binding / microtubule organizing center / cytoplasmic microtubule organization / spindle pole / actin cytoskeleton ...mitotic spindle microtubule / polar microtubule / gamma-tubulin complex / dense body / microtubule nucleation / gamma-tubulin binding / microtubule organizing center / cytoplasmic microtubule organization / spindle pole / actin cytoskeleton / microtubule / cytoskeleton / focal adhesion / centrosome / GTP binding / ATP binding / nucleus / plasma membrane / cytoplasm Similarity search - Function | |||||||||
Biological species | Xenopus laevis (African clawed frog) / African clawed frog (African clawed frog) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.8 Å | |||||||||
Authors | Zupa E / Pfeffer S | |||||||||
Citation | Journal: Nature / Year: 2020 Title: Insights into the assembly and activation of the microtubule nucleator γ-TuRC. Authors: Peng Liu / Erik Zupa / Annett Neuner / Anna Böhler / Justus Loerke / Dirk Flemming / Thomas Ruppert / Till Rudack / Christoph Peter / Christian Spahn / Oliver J Gruss / Stefan Pfeffer / Elmar Schiebel / Abstract: Microtubules are dynamic polymers of α- and β-tubulin and have crucial roles in cell signalling, cell migration, intracellular transport and chromosome segregation. They assemble de novo from αβ- ...Microtubules are dynamic polymers of α- and β-tubulin and have crucial roles in cell signalling, cell migration, intracellular transport and chromosome segregation. They assemble de novo from αβ-tubulin dimers in an essential process termed microtubule nucleation. Complexes that contain the protein γ-tubulin serve as structural templates for the microtubule nucleation reaction. In vertebrates, microtubules are nucleated by the 2.2-megadalton γ-tubulin ring complex (γ-TuRC), which comprises γ-tubulin, five related γ-tubulin complex proteins (GCP2-GCP6) and additional factors. GCP6 is unique among the GCP proteins because it carries an extended insertion domain of unknown function. Our understanding of microtubule formation in cells and tissues is limited by a lack of high-resolution structural information on the γ-TuRC. Here we present the cryo-electron microscopy structure of γ-TuRC from Xenopus laevis at 4.8 Å global resolution, and identify a 14-spoked arrangement of GCP proteins and γ-tubulins in a partially flexible open left-handed spiral with a uniform sequence of GCP variants. By forming specific interactions with other GCP proteins, the GCP6-specific insertion domain acts as a scaffold for the assembly of the γ-TuRC. Unexpectedly, we identify actin as a bona fide structural component of the γ-TuRC with functional relevance in microtubule nucleation. The spiral geometry of γ-TuRC is suboptimal for microtubule nucleation and a controlled conformational rearrangement of the γ-TuRC is required for its activation. Collectively, our cryo-electron microscopy reconstructions provide detailed insights into the molecular organization, assembly and activation mechanism of vertebrate γ-TuRC, and will serve as a framework for the mechanistic understanding of fundamental biological processes associated with microtubule nucleation, such as meiotic and mitotic spindle formation and centriole biogenesis. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_10491.map.gz | 5.1 MB | EMDB map data format | |
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Header (meta data) | emd-10491-v30.xml emd-10491.xml | 34.7 KB 34.7 KB | Display Display | EMDB header |
Images | emd_10491.png | 242.4 KB | ||
Others | emd_10491_additional.map.gz | 34 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-10491 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-10491 | HTTPS FTP |
-Related structure data
Related structure data | 6tf9MC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_10491.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Cryo-EM single particle analysis reconstruction of the vertebrate gamma-Tubulin Ring Complex | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Additional map: Cryo-EM single particle analysis reconstruction of the vertebrate...
File | emd_10491_additional.map | ||||||||||||
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Annotation | Cryo-EM single particle analysis reconstruction of the vertebrate gamma-Tubulin Ring Complex filtered according to local resolution | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Vertebrate gamma-Tubulin Ring Complex
+Supramolecule #1: Vertebrate gamma-Tubulin Ring Complex
+Macromolecule #1: Helix 1
+Macromolecule #2: Belt helices 1,2,3,4
+Macromolecule #3: Belt helix 5
+Macromolecule #4: Belt helix 6
+Macromolecule #5: Belt helix 7
+Macromolecule #6: Belt helices 8,9,10
+Macromolecule #7: Belt helices 11,12
+Macromolecule #8: Belt helices 13,14,15 and Helix 2
+Macromolecule #9: Belt helix 16
+Macromolecule #10: Gamma-tubulin complex component 3 homolog
+Macromolecule #11: Gamma-tubulin complex component 2
+Macromolecule #12: Gamma tubulin ring protein
+Macromolecule #13: Tubulin gamma-1 chain
+Macromolecule #14: Gamma-tubulin complex component
+Macromolecule #15: Gamma-tubulin complex component
+Macromolecule #16: Belt helix 17
+Macromolecule #17: Actin, cytoplasmic 1
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.011 mg/mL | ||||||||||||||||||||||||
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Buffer | pH: 8 Component:
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Grid | Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE | ||||||||||||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 70 % / Chamber temperature: 295 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 42000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 4 / Number real images: 9463 / Average electron dose: 46.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Particle selection | Number selected: 5482328 |
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CTF correction | Software - Name: RELION (ver. 3.0 Beta) |
Startup model | Type of model: OTHER Details: 3D initial model from manually selected particles in Relion |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0 Beta) |
Final 3D classification | Software - Name: RELION (ver. 3.0 Beta) |
Final angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0 Beta) |
Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0 Beta) / Number images used: 46096 |