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Yorodumi- EMDB-17227: Cryo-EM structure of the yeast Inner kinetochore bound to a CENP-... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-17227 | |||||||||||||||
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Title | Cryo-EM structure of the yeast Inner kinetochore bound to a CENP-A nucleosome. | |||||||||||||||
Map data | ||||||||||||||||
Sample |
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Keywords | kinetochore / point centromere / CENP-A nucleosome / topological entrapment / centromeric DNA / CELL CYCLE | |||||||||||||||
Function / homology | Function and homology information Cbf1-Met4-Met28 complex / regulation of sulfur metabolic process / negative regulation of kinetochore assembly / 2-micrometer circle DNA / 2-micrometer plasmid partitioning / negative regulation of meiotic DNA double-strand break formation involved in reciprocal meiotic recombination / COMA complex / maintenance of meiotic sister chromatid cohesion / RAVE complex / Iron uptake and transport ...Cbf1-Met4-Met28 complex / regulation of sulfur metabolic process / negative regulation of kinetochore assembly / 2-micrometer circle DNA / 2-micrometer plasmid partitioning / negative regulation of meiotic DNA double-strand break formation involved in reciprocal meiotic recombination / COMA complex / maintenance of meiotic sister chromatid cohesion / RAVE complex / Iron uptake and transport / CBF3 complex / HDMs demethylate histones / regulation of transcription by galactose / regulation of sulfur amino acid metabolic process / cellular response to methylmercury / PKMTs methylate histone lysines / Mis6-Sim4 complex / vacuolar proton-transporting V-type ATPase complex assembly / centromere complex assembly / meiotic sister chromatid segregation / establishment of meiotic sister chromatid cohesion / septin ring assembly / ascospore formation / HATs acetylate histones / RNA polymerase I upstream activating factor complex / Condensation of Prophase Chromosomes / SIRT1 negatively regulates rRNA expression / attachment of spindle microtubules to kinetochore / 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 / CENP-A containing chromatin assembly / HDACs deacetylate histones / regulation of exit from mitosis / outer kinetochore / protein localization to chromosome, centromeric region / establishment of mitotic sister chromatid cohesion / kinetochore assembly / condensed chromosome, centromeric region / regulation of metabolic process / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / protein localization to kinetochore / replication fork protection complex / spindle pole body / positive regulation of glucose transmembrane transport / protein neddylation / Oxidative Stress Induced Senescence / RMTs methylate histone arginines / postreplication repair / SUMOylation of chromatin organization proteins / mitotic intra-S DNA damage checkpoint signaling / vacuolar acidification / silent mating-type cassette heterochromatin formation / mitochondrial fusion / exit from mitosis / DNA binding, bending / SCF ubiquitin ligase complex / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / positive regulation of transcription by RNA polymerase I / mitotic spindle assembly checkpoint signaling / Orc1 removal from chromatin / RNA Polymerase I Promoter Escape / nucleolar large rRNA transcription by RNA polymerase I / mitotic sister chromatid segregation / DNA replication origin binding / cullin family protein binding / Estrogen-dependent gene expression / Antigen processing: Ubiquitination & Proteasome degradation / rRNA transcription / chromosome, centromeric region / subtelomeric heterochromatin formation / DNA replication initiation / regulation of protein-containing complex assembly / heterochromatin organization / Ub-specific processing proteases / endomembrane system / protein localization to CENP-A containing chromatin / negative regulation of cytoplasmic translation / CENP-A containing nucleosome / nucleosomal DNA binding / regulation of mitotic cell cycle / meiotic cell cycle / chromosome segregation / kinetochore / DNA-binding transcription repressor activity, RNA polymerase II-specific / G1/S transition of mitotic cell cycle / structural constituent of chromatin / G2/M transition of mitotic cell cycle / nucleosome / nucleosome assembly / chromatin organization / mitotic cell cycle / ubiquitin-dependent protein catabolic process / protein-containing complex assembly / DNA-binding transcription activator activity, RNA polymerase II-specific / RNA polymerase II-specific DNA-binding transcription factor binding / sequence-specific DNA binding / chromosome, telomeric region / protein dimerization activity Similarity search - Function | |||||||||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.7 Å | |||||||||||||||
Authors | Dendooven TD / Zhang Z / Yang J / McLaughlin S / Schwabb J / Scheres S / Yatskevich S / Barford D | |||||||||||||||
Funding support | United Kingdom, Germany, 4 items
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Citation | Journal: Sci Adv / Year: 2023 Title: Cryo-EM structure of the complete inner kinetochore of the budding yeast point centromere. Authors: Tom Dendooven / Ziguo Zhang / Jing Yang / Stephen H McLaughlin / Johannes Schwab / Sjors H W Scheres / Stanislau Yatskevich / David Barford / Abstract: The point centromere of budding yeast specifies assembly of the large kinetochore complex to mediate chromatid segregation. Kinetochores comprise the centromere-associated inner kinetochore (CCAN) ...The point centromere of budding yeast specifies assembly of the large kinetochore complex to mediate chromatid segregation. Kinetochores comprise the centromere-associated inner kinetochore (CCAN) complex and the microtubule-binding outer kinetochore KNL1-MIS12-NDC80 (KMN) network. The budding yeast inner kinetochore also contains the DNA binding centromere-binding factor 1 (CBF1) and CBF3 complexes. We determined the cryo-electron microscopy structure of the yeast inner kinetochore assembled onto the centromere-specific centromere protein A nucleosomes (CENP-A). This revealed a central CENP-A with extensively unwrapped DNA ends. These free DNA duplexes bind two CCAN protomers, one of which entraps DNA topologically, positioned on the centromere DNA element I (CDEI) motif by CBF1. The two CCAN protomers are linked through CBF3 forming an arch-like configuration. With a structural mechanism for how CENP-A can also be linked to KMN involving only CENP-QU, we present a model for inner kinetochore assembly onto a point centromere and how it organizes the outer kinetochore for chromosome attachment to the mitotic spindle. | |||||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_17227.map.gz | 96.9 MB | EMDB map data format | |
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Header (meta data) | emd-17227-v30.xml emd-17227.xml | 46.9 KB 46.9 KB | Display Display | EMDB header |
Images | emd_17227.png | 83.3 KB | ||
Others | emd_17227_additional_1.map.gz emd_17227_half_map_1.map.gz emd_17227_half_map_2.map.gz | 29.6 MB 131.5 MB 131.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-17227 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-17227 | HTTPS FTP |
-Validation report
Summary document | emd_17227_validation.pdf.gz | 936.6 KB | Display | EMDB validaton report |
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Full document | emd_17227_full_validation.pdf.gz | 936.1 KB | Display | |
Data in XML | emd_17227_validation.xml.gz | 14.5 KB | Display | |
Data in CIF | emd_17227_validation.cif.gz | 17 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-17227 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-17227 | HTTPS FTP |
-Related structure data
Related structure data | 8ow1MC 8ovwC 8ovxC 8ow0C C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_17227.map.gz / Format: CCP4 / Size: 166.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 1.08 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: #1
File | emd_17227_additional_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_17227_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_17227_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
+Entire : A complex of CBF1-CCAN bound to centromeric C0N3 DNA
+Supramolecule #1: A complex of CBF1-CCAN bound to centromeric C0N3 DNA
+Macromolecule #1: Centromere-binding protein 1
+Macromolecule #2: Inner kinetochore subunit CTF3
+Macromolecule #3: Inner kinetochore subunit MCM22
+Macromolecule #4: Inner kinetochore subunit MCM16
+Macromolecule #5: Inner kinetochore subunit IML3
+Macromolecule #6: Inner kinetochore subunit CHL4
+Macromolecule #7: Centromere DNA-binding protein complex CBF3 subunit C
+Macromolecule #8: Centromere DNA-binding protein complex CBF3 subunit B
+Macromolecule #9: Suppressor of kinetochore protein 1
+Macromolecule #10: Inner kinetochore subunit CTF19
+Macromolecule #11: Inner kinetochore subunit OKP1
+Macromolecule #12: Inner kinetochore subunit MCM21
+Macromolecule #13: Inner kinetochore subunit CNN1
+Macromolecule #14: Inner kinetochore subunit AME1
+Macromolecule #15: Inner kinetochore subunit WIP1
+Macromolecule #16: Inner kinetochore subunit NKP1
+Macromolecule #17: Inner kinetochore subunit NKP2
+Macromolecule #20: Histone H4
+Macromolecule #21: Histone H2B.1
+Macromolecule #22: Histone H3-like centromeric protein CSE4
+Macromolecule #23: Histone H2A.1
+Macromolecule #18: C0N3
+Macromolecule #19: C0N3
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 40.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.6 µm / Nominal defocus min: 1.0 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: NONE |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 108672 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |