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Yorodumi- EMDB-20839: Structure of a Yeast Centromeric Nucleosome at 2.7 Angstrom resolution -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-20839 | |||||||||
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Title | Structure of a Yeast Centromeric Nucleosome at 2.7 Angstrom resolution | |||||||||
Map data | Sharpened and masked map of CEN-NCP contoured at 0.16 level | |||||||||
Sample |
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Keywords | Histones / Nucleosome / Centromere / Kinetochore / Yeast / CELL CYCLE | |||||||||
Function / homology | Function and homology information 2-micrometer circle DNA / 2-micrometer plasmid partitioning / HDMs demethylate histones / PKMTs methylate histone lysines / Condensation of Prophase Chromosomes / SIRT1 negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / centromeric DNA binding / Assembly of the ORC complex at the origin of replication / HDACs deacetylate histones ...2-micrometer circle DNA / 2-micrometer plasmid partitioning / HDMs demethylate histones / PKMTs methylate histone lysines / Condensation of Prophase Chromosomes / SIRT1 negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / centromeric DNA binding / Assembly of the ORC complex at the origin of replication / HDACs deacetylate histones / kinetochore assembly / condensed chromosome, centromeric region / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / Oxidative Stress Induced Senescence / RMTs methylate histone arginines / RNA Polymerase I Promoter Escape / mitotic sister chromatid segregation / Estrogen-dependent gene expression / rRNA transcription / protein localization to CENP-A containing chromatin / CENP-A containing nucleosome / structural constituent of chromatin / nucleosome / nucleosome assembly / sequence-specific DNA binding / protein heterodimerization activity / DNA repair / DNA binding / nucleus Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) / Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (yeast) / unidentified (others) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.7 Å | |||||||||
Authors | Migl D / Kschonsak M | |||||||||
Funding support | United States, 2 items
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Citation | Journal: Structure / Year: 2020 Title: Cryoelectron Microscopy Structure of a Yeast Centromeric Nucleosome at 2.7 Å Resolution. Authors: David Migl / Marc Kschonsak / Christopher P Arthur / Yadana Khin / Stephen C Harrison / Claudio Ciferri / Yoana N Dimitrova / Abstract: Kinetochores mediate chromosome segregation during cell division. They assemble on centromeric nucleosomes and capture spindle microtubules. In budding yeast, a kinetochore links a single nucleosome, ...Kinetochores mediate chromosome segregation during cell division. They assemble on centromeric nucleosomes and capture spindle microtubules. In budding yeast, a kinetochore links a single nucleosome, containing the histone variant Cse4 instead of H3, with a single microtubule. Conservation of most kinetochore components from yeast to metazoans suggests that the yeast kinetochore represents a module of the more complex metazoan arrangements. We describe here a streamlined protocol for reconstituting a yeast centromeric nucleosome and a systematic exploration of cryo-grid preparation. These developments allowed us to obtain a high-resolution cryoelectron microscopy reconstruction. As suggested by previous work, fewer base pairs are in tight association with the histone octamer than there are in canonical nucleosomes. Weak binding of the end DNA sequences may contribute to specific recognition by other inner kinetochore components. The centromeric nucleosome structure and the strategies we describe will facilitate studies of many other aspects of kinetochore assembly and chromatin biochemistry. | |||||||||
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_20839.map.gz | 24.3 MB | EMDB map data format | |
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Header (meta data) | emd-20839-v30.xml emd-20839.xml | 29.7 KB 29.7 KB | Display Display | EMDB header |
Images | emd_20839.png | 123.6 KB | ||
Filedesc metadata | emd-20839.cif.gz | 6.5 KB | ||
Others | emd_20839_additional_1.map.gz emd_20839_additional_2.map.gz emd_20839_additional_3.map.gz emd_20839_half_map_1.map.gz emd_20839_half_map_2.map.gz | 24.8 MB 25.1 MB 25.1 MB 8.9 MB 8.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-20839 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-20839 | HTTPS FTP |
-Validation report
Summary document | emd_20839_validation.pdf.gz | 927.7 KB | Display | EMDB validaton report |
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Full document | emd_20839_full_validation.pdf.gz | 927.3 KB | Display | |
Data in XML | emd_20839_validation.xml.gz | 10.6 KB | Display | |
Data in CIF | emd_20839_validation.cif.gz | 12.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-20839 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-20839 | HTTPS FTP |
-Related structure data
Related structure data | 6uphMC 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_20839.map.gz / Format: CCP4 / Size: 27 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Sharpened and masked map of CEN-NCP contoured at 0.16 level | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.849 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Additional map: Gaussian filtered unmasked map
File | emd_20839_additional_1.map | ||||||||||||
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Annotation | Gaussian filtered unmasked map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Masked map of CEN-NCP contoured at 1.1 level
File | emd_20839_additional_2.map | ||||||||||||
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Annotation | Masked map of CEN-NCP contoured at 1.1 level | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Unmasked map of CEN-NCP contoured at 1.3 level
File | emd_20839_additional_3.map | ||||||||||||
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Annotation | Unmasked map of CEN-NCP contoured at 1.3 level | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Masked halfmap 2
File | emd_20839_half_map_1.map | ||||||||||||
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Annotation | Masked halfmap 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Masked halfmap 1
File | emd_20839_half_map_2.map | ||||||||||||
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Annotation | Masked halfmap 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Yeast Centromeric Nucleosome
+Supramolecule #1: Yeast Centromeric Nucleosome
+Supramolecule #2: Histone H3-like centromeric protein CSE4
+Supramolecule #3: Histone H4, Histone H2A, Histone H2B.1
+Supramolecule #4: DNA
+Macromolecule #1: Histone H3-like centromeric protein CSE4
+Macromolecule #2: Histone H4
+Macromolecule #3: Histone H2A
+Macromolecule #4: Histone H2B.1
+Macromolecule #5: DNA (119-MER)
+Macromolecule #6: DNA (119-MER)
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 1 mg/mL |
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Buffer | pH: 7.5 |
Grid | Model: Quantifoil, UltrAuFoil, R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 20 sec. |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 1.249 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: INSILICO MODEL |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cisTEM / Number images used: 265380 |
Initial angle assignment | Type: RANDOM ASSIGNMENT / Software - Name: cisTEM |
Final angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: cisTEM |