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Yorodumi- EMDB-10744: Microtubule Nucleation by Single Human gamma-TuRC in a Partly Ope... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-10744 | |||||||||
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Title | Microtubule Nucleation by Single Human gamma-TuRC in a Partly Open Asymmetric Conformation | |||||||||
Map data | Cryo-EM structure of human gamma-TuRC | |||||||||
Sample |
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Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.0 Å | |||||||||
Authors | Locke J / Costa A | |||||||||
Funding support | United Kingdom, 1 items
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Citation | Journal: Dev Cell / Year: 2020 Title: Microtubule Nucleation Properties of Single Human γTuRCs Explained by Their Cryo-EM Structure. Authors: Tanja Consolati / Julia Locke / Johanna Roostalu / Zhuo Angel Chen / Julian Gannon / Jayant Asthana / Wei Ming Lim / Fabrizio Martino / Milos A Cvetkovic / Juri Rappsilber / Alessandro Costa / Thomas Surrey / Abstract: The γ-tubulin ring complex (γTuRC) is the major microtubule nucleator in cells. The mechanism of its regulation is not understood. We purified human γTuRC and measured its nucleation properties in ...The γ-tubulin ring complex (γTuRC) is the major microtubule nucleator in cells. The mechanism of its regulation is not understood. We purified human γTuRC and measured its nucleation properties in a total internal reflection fluorescence (TIRF) microscopy-based real-time nucleation assay. We find that γTuRC stably caps the minus ends of microtubules that it nucleates stochastically. Nucleation is inefficient compared with microtubule elongation. The 4 Å resolution cryoelectron microscopy (cryo-EM) structure of γTuRC, combined with crosslinking mass spectrometry analysis, reveals an asymmetric conformation with only part of the complex in a "closed" conformation matching the microtubule geometry. Actin in the core of the complex, and MZT2 at the outer perimeter of the closed part of γTuRC appear to stabilize the closed conformation. The opposite side of γTuRC is in an "open," nucleation-incompetent conformation, leading to a structural asymmetry explaining the low nucleation efficiency of purified human γTuRC. Our data suggest possible regulatory mechanisms for microtubule nucleation by γTuRC closure. | |||||||||
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_10744.map.gz | 34.7 MB | EMDB map data format | |
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Header (meta data) | emd-10744-v30.xml emd-10744.xml | 12.8 KB 12.8 KB | Display Display | EMDB header |
Images | emd_10744.png | 208 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-10744 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-10744 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_10744.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Cryo-EM structure of human gamma-TuRC | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.08 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : gamma-tubulin ring complex
Entire | Name: gamma-tubulin ring complex |
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Components |
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-Supramolecule #1: gamma-tubulin ring complex
Supramolecule | Name: gamma-tubulin ring complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Homo sapiens (human) / Recombinant cell: HeLa-Kyoto cells |
Molecular weight | Theoretical: 2.2 MDa |
-Macromolecule #1: gamma-tubulin ring complex
Macromolecule | Name: gamma-tubulin ring complex / type: protein_or_peptide / ID: 1 Details: Complex consists of 5x native GCP2/GCP with mBFP tag, 5x GCP3, 2x GCP4, 1x GCP5, 1x GCP6 and other factors Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MSEFRIHHDV NELLSLLRVH GGDGAEVYID LLQKNRTPYV TTTVSAHSAK VKIAEFSRTP EDFLKKYDEL KSKNTRNLDP LVYLLSKLTE DKETLQYLQQ NAKERAELAA AAVGSSTTSI NVPAAASKIS MQELEELRKQ LGSVATGSTL QQSLELKRKM LRDKQNKKNS ...String: MSEFRIHHDV NELLSLLRVH GGDGAEVYID LLQKNRTPYV TTTVSAHSAK VKIAEFSRTP EDFLKKYDEL KSKNTRNLDP LVYLLSKLTE DKETLQYLQQ NAKERAELAA AAVGSSTTSI NVPAAASKIS MQELEELRKQ LGSVATGSTL QQSLELKRKM LRDKQNKKNS GQHLPIFPAW VYERPALIGD FLIGAGISTD TALPIGTLPL ASQESAVVED LLYVLVGVDG RYVSAQPLAG RQSRTFLVDP NLDLSIRELV HRILPVAASY SAVTRFIEEK SSFEYGQVNH ALAAAMRTLV KEHLILVSQL EQLHRQGLLS LQKLWFYIQP AMRTMDILAS LATSVDKGEC LGGSTLSLLH DRSFSYTGDS QAQELCLYLT KAASAPYFEV LEKWIYRGII HDPYSEFMVE EHELRKERIQ EDYNDKYWDQ RYTIVQQQIP SFLQKMADKI LSTGKYLNVV RECGHDVTCP VAKEIIYTLK ERAYVEQIEK AFNYASKVLL DFLMEEKELV AHLRSIKRYF LMDQGDFFVH FMDLAEEELR KPVEDITPPR LEALLELALR MSTANTDPFK DDLKIDLMPH DLITQLLRVL AIETKQEKAM AHADPTELAL SGLEAFSFDY IVKWPLSLII NRKALTRYQM LFRHMFYCKH VERQLCSVWI SNKTAKQHSL HSAQWFAGAF TLRQRMLNFV QNIQYYMMFE VMEPTWHILE KNLKSASNID DVLGHHTGFL DTCLKDCMLT NPELLKVFSK LMSVCVMFTN CMQKFTQSMK LDGELGGQTL EHSTVLGLPA GAEERARKEL ARKHLAEHAD TVQLVSGFEA TINKFDKNFS AHLLDLLARL SIYSTSDCEH GMASVISRLD FNGFYTERLE RLSAERSQKA TPQVPVLRGP PAPAPRVAVT AQGGGGGENL YFQGGGGGGS EELIKENMHM KLYMEGTVDN HHFKCTSEGE GKPYEGTQTM RIKVVEGGPL PFAFDILATS FLYGSKTFIN HTQGIPDFFK QSFPEGFTWE RVTTYEDGGV LTATQDTSLQ DGCLIYNVKI RGVNFTSNGP VMQKKTLGWE AFTETLYPAD GGLEGRNDMA LKLVGGSHLI ANIKTTYRSK KPAKNLKMPG VYYVDYRLER IKEANNETYV EQHEVAVARY CDLPSKLGHK LNGGGGGGLN DIFEAQKIEW HE |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 |
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Grid | Model: Homemade / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 298 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 | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 130000 |
Specialist optics | Energy filter - Name: GIF Quantum LS |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Image recording | Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 2 / Number real images: 2400 / Average exposure time: 9.0 sec. / Average electron dose: 50.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
CTF correction | Software - Name: Gctf (ver. v.1.18) |
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Startup model | Type of model: OTHER / Details: ab initio |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |
Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 522496 |