+Open data
-Basic information
Entry | Database: PDB / ID: 9eoj | |||||||||||||||||||||
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Title | Vertebrate microtubule-capping gamma-tubulin ring complex | |||||||||||||||||||||
Components |
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Keywords | CELL CYCLE / cytoskeleton / microtubule / microtubule nucleation / complex / template / cap / gamma-tubulin / gamma-tubulin ring complex | |||||||||||||||||||||
Function / homology | Function and homology information gamma-tubulin complex localization / equatorial microtubule organizing center / mitotic spindle microtubule / gamma-tubulin ring complex / microtubule minus-end binding / polar microtubule / gamma-tubulin complex / meiotic spindle organization / microtubule nucleation / gamma-tubulin binding ...gamma-tubulin complex localization / equatorial microtubule organizing center / mitotic spindle microtubule / gamma-tubulin ring complex / microtubule minus-end binding / polar microtubule / gamma-tubulin complex / meiotic spindle organization / microtubule nucleation / gamma-tubulin binding / mitotic sister chromatid segregation / spindle assembly / cytoplasmic microtubule organization / mitotic spindle organization / meiotic cell cycle / structural constituent of cytoskeleton / spindle pole / spindle / mitotic cell cycle / microtubule / centrosome / GTP binding / nucleus / cytoplasm Similarity search - Function | |||||||||||||||||||||
Biological species | Xenopus laevis (African clawed frog) | |||||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 17 Å | |||||||||||||||||||||
Authors | Vermeulen, B.J.A. / Pfeffer, S. | |||||||||||||||||||||
Funding support | Germany, 6items
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Citation | Journal: EMBO J / Year: 2024 Title: γ-TuRC asymmetry induces local protofilament mismatch at the RanGTP-stimulated microtubule minus end. Authors: Bram Ja Vermeulen / Anna Böhler / Qi Gao / Annett Neuner / Erik Župa / Zhenzhen Chu / Martin Würtz / Ursula Jäkle / Oliver J Gruss / Stefan Pfeffer / Elmar Schiebel / Abstract: The γ-tubulin ring complex (γ-TuRC) is a structural template for de novo microtubule assembly from α/β-tubulin units. The isolated vertebrate γ-TuRC assumes an asymmetric, open structure ...The γ-tubulin ring complex (γ-TuRC) is a structural template for de novo microtubule assembly from α/β-tubulin units. The isolated vertebrate γ-TuRC assumes an asymmetric, open structure deviating from microtubule geometry, suggesting that γ-TuRC closure may underlie regulation of microtubule nucleation. Here, we isolate native γ-TuRC-capped microtubules from Xenopus laevis egg extract nucleated through the RanGTP-induced pathway for spindle assembly and determine their cryo-EM structure. Intriguingly, the microtubule minus end-bound γ-TuRC is only partially closed and consequently, the emanating microtubule is locally misaligned with the γ-TuRC and asymmetric. In the partially closed conformation of the γ-TuRC, the actin-containing lumenal bridge is locally destabilised, suggesting lumenal bridge modulation in microtubule nucleation. The microtubule-binding protein CAMSAP2 specifically binds the minus end of γ-TuRC-capped microtubules, indicating that the asymmetric minus end structure may underlie recruitment of microtubule-modulating factors for γ-TuRC release. Collectively, we reveal a surprisingly asymmetric microtubule minus end protofilament organisation diverging from the regular microtubule structure, with direct implications for the kinetics and regulation of nucleation and subsequent modulation of microtubules during spindle assembly. | |||||||||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 9eoj.cif.gz | 2.5 MB | Display | PDBx/mmCIF format |
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PDB format | pdb9eoj.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 9eoj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 9eoj_validation.pdf.gz | 1.7 MB | Display | wwPDB validaton report |
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Full document | 9eoj_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 9eoj_validation.xml.gz | 310.4 KB | Display | |
Data in CIF | 9eoj_validation.cif.gz | 505.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/eo/9eoj ftp://data.pdbj.org/pub/pdb/validation_reports/eo/9eoj | HTTPS FTP |
-Related structure data
Related structure data | 19861MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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-Components
-Protein , 2 types, 16 molecules BDThiklmnopqrstw
#1: Protein | Mass: 7749.854 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Xenopus laevis (African clawed frog) / References: UniProt: Q5U4M5 #5: Protein | Mass: 51226.719 Da / Num. of mol.: 14 / Source method: isolated from a natural source / Source: (natural) Xenopus laevis (African clawed frog) / References: UniProt: P23330 |
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-Gamma-tubulin complex ... , 5 types, 14 molecules QcdefRYZabSUVW
#2: Protein | Mass: 103789.352 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) Xenopus laevis (African clawed frog) / References: UniProt: O73787 #3: Protein | Mass: 103468.312 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) Xenopus laevis (African clawed frog) / References: UniProt: A0A8J0T6B8 #4: Protein | | Mass: 193069.141 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Xenopus laevis (African clawed frog) / References: UniProt: A0A974HT83 #6: Protein | | Mass: 117577.633 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Xenopus laevis (African clawed frog) / References: UniProt: A0A1L8HGZ5 #7: Protein | Mass: 76122.961 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Xenopus laevis (African clawed frog) / References: UniProt: Q642S3 |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Vertebrate microtubule-capping gamma-tubulin ring complex Type: COMPLEX Details: Vertebrate microtubule-capping gamma-tubulin ring complex induced through the RanGTP spindle assembly pathway and isolated from Xenopus laevis egg extract Entity ID: all / Source: NATURAL |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: Xenopus laevis (African clawed frog) |
Buffer solution | pH: 6.8 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/1 |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 295 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 33000 X / Nominal defocus max: 3000 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 43 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
EM imaging optics | Energyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 17 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 8497 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT | ||||||||||||||||||||||||||||||||||||||||
Atomic model building |
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