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- PDB-6uph: Structure of a Yeast Centromeric Nucleosome at 2.7 Angstrom resolution -
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Open data
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Basic information
Entry | Database: PDB / ID: 6uph | |||||||||
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Title | Structure of a Yeast Centromeric Nucleosome at 2.7 Angstrom resolution | |||||||||
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![]() | CELL CYCLE / Histones / Nucleosome / Centromere / Kinetochore / Yeast | |||||||||
Function / homology | ![]() 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 | ![]() ![]() ![]() unidentified (others) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.7 Å | |||||||||
![]() | Migl, D. / Kschonsak, M. / Arthur, C.P. / Khin, Y. / Harrison, S.C. / Ciferri, C. / Dimitrova, Y.N. | |||||||||
Funding support | ![]()
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![]() | ![]() 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 |
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 262 KB | Display | ![]() |
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PDB format | ![]() | 191.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.3 MB | Display | ![]() |
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Full document | ![]() | 1.3 MB | Display | |
Data in XML | ![]() | 31.7 KB | Display | |
Data in CIF | ![]() | 48.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 20839MC M: map data used to model this data C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Components
-Protein , 4 types, 8 molecules AEBFCGDH
#1: Protein | Mass: 26885.434 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: ATCC 204508 / S288c / Gene: CSE4, CSL2, YKL049C, YKL262 / Production host: ![]() ![]() #2: Protein | Mass: 13332.434 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37 Gene: KLLA0_E08647g, KLLA0_E17601g / Production host: ![]() ![]() #3: Protein | Mass: 15739.005 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37 Gene: HTA1, KLLA0E17413g, HTA2, KLLA0F13332g / Production host: ![]() ![]() #4: Protein | Mass: 16219.361 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37 Gene: HTB1, KLLA0F13310g / Production host: ![]() ![]() |
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-DNA chain , 2 types, 2 molecules IJ
#5: DNA chain | Mass: 45138.770 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) unidentified (others) / Production host: ![]() ![]() |
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#6: DNA chain | Mass: 45610.043 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) unidentified (others) / Production host: ![]() ![]() |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
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Molecular weight | Value: 240 kDa/nm / Experimental value: NO | ||||||||||||||||||||||||||||||
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Buffer solution | pH: 7.5 | ||||||||||||||||||||||||||||||
Specimen | Conc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||||||||
Specimen support | Grid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil, UltrAuFoil, R1.2/1.3 | ||||||||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K |
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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: ![]() |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 1.249 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
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Processing
Software | Name: PHENIX / Version: 1.14_3260: / Classification: refinement | ||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 265380 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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