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Yorodumi- EMDB-19778: in situ subtomogram average of C. elegans microtubules in mitotic... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-19778 | |||||||||
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Title | in situ subtomogram average of C. elegans microtubules in mitotic centrosomes | |||||||||
Map data | C. elegans microtubule average from mitotic centrosomes. | |||||||||
Sample |
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Keywords | Microtubule / 11-protofilaments / cryo-ET / cryo-FIB / C. elegans / mitosis / centrosome / CELL CYCLE | |||||||||
Biological species | Caenorhabditis elegans (invertebrata) | |||||||||
Method | subtomogram averaging / cryo EM / Resolution: 26.0 Å | |||||||||
Authors | Tollervey F / Rios MU / Zagoriy I / Woodruff JB / Mahamid J | |||||||||
Funding support | European Union, 1 items
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Citation | Journal: bioRxiv / Year: 2024 Title: Native molecular architectures of centrosomes in embryos. Authors: Fergus Tollervey / Manolo U Rios / Evgenia Zagoriy / Jeffrey B Woodruff / Julia Mahamid / Abstract: Centrosomes organize microtubules that are essential for mitotic divisions in animal cells. They consist of centrioles surrounded by Pericentriolar Material (PCM). Questions related to mechanisms of ...Centrosomes organize microtubules that are essential for mitotic divisions in animal cells. They consist of centrioles surrounded by Pericentriolar Material (PCM). Questions related to mechanisms of centriole assembly, PCM organization, and microtubule formation remain unanswered, in part due to limited availability of molecular-resolution structural analyses . Here, we use cryo-electron tomography to visualize centrosomes across the cell cycle in cells isolated from embryos. We describe a pseudo-timeline of centriole assembly and identify distinct structural features including a cartwheel in daughter centrioles, and incomplete microtubule doublets surrounded by a star-shaped density in mother centrioles. We find that centriole and PCM microtubules differ in protofilament number (13 versus 11) indicating distinct nucleation mechanisms. This difference could be explained by atypical γ-tubulin ring complexes with 11-fold symmetry identified at the minus ends of short PCM microtubules. We further characterize a porous and disordered network that forms the interconnected PCM. Thus, our work builds a three-dimensional structural atlas that helps explain how centrosomes assemble, grow, and achieve function. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_19778.map.gz | 757.7 KB | EMDB map data format | |
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Header (meta data) | emd-19778-v30.xml emd-19778.xml | 13.9 KB 13.9 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_19778_fsc.xml | 3.4 KB | Display | FSC data file |
Images | emd_19778.png | 51.1 KB | ||
Masks | emd_19778_msk_1.map | 1.4 MB | Mask map | |
Filedesc metadata | emd-19778.cif.gz | 4.5 KB | ||
Others | emd_19778_half_map_1.map.gz emd_19778_half_map_2.map.gz | 1.2 MB 1.2 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-19778 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-19778 | HTTPS FTP |
-Validation report
Summary document | emd_19778_validation.pdf.gz | 709.9 KB | Display | EMDB validaton report |
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Full document | emd_19778_full_validation.pdf.gz | 709.5 KB | Display | |
Data in XML | emd_19778_validation.xml.gz | 8.5 KB | Display | |
Data in CIF | emd_19778_validation.cif.gz | 10.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-19778 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-19778 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_19778.map.gz / Format: CCP4 / Size: 1.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | C. elegans microtubule average from mitotic centrosomes. | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 6.7404 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_19778_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_19778_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_19778_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Dissociated C. elegans embryonic cells
Entire | Name: Dissociated C. elegans embryonic cells |
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Components |
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-Supramolecule #1: Dissociated C. elegans embryonic cells
Supramolecule | Name: Dissociated C. elegans embryonic cells / type: cell / ID: 1 / Parent: 0 |
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Source (natural) | Organism: Caenorhabditis elegans (invertebrata) / Tissue: Embryo |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | subtomogram averaging |
Aggregation state | cell |
-Sample preparation
Buffer | pH: 7.4 |
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Grid | Model: Quantifoil / Material: GOLD / Mesh: 200 / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 45 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.037 kPa |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Phase plate: VOLTA PHASE PLATE / Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: COUNTING / Average electron dose: 120.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 4.5 µm / Nominal defocus min: 2.5 µm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |