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Open data
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Basic information
Entry | Database: PDB / ID: 6qld | ||||||||||||
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Title | Structure of inner kinetochore CCAN-Cenp-A complex | ||||||||||||
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![]() | DNA BINDING PROTEIN / inner kinetochore / DNA / nucleosome | ||||||||||||
Function / homology | ![]() 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 / HDMs demethylate histones / PKMTs methylate histone lysines / Mis6-Sim4 complex / centromere complex assembly / meiotic sister chromatid segregation ...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 / HDMs demethylate histones / PKMTs methylate histone lysines / Mis6-Sim4 complex / centromere complex assembly / meiotic sister chromatid segregation / establishment of meiotic sister chromatid cohesion / ascospore formation / spindle attachment to meiosis I kinetochore / 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 / outer kinetochore / protein localization to chromosome, centromeric region / establishment of mitotic sister chromatid cohesion / kinetochore assembly / condensed chromosome, centromeric region / attachment of mitotic spindle microtubules to kinetochore / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / spindle pole body / protein localization to kinetochore / replication fork protection complex / RMTs methylate histone arginines / Oxidative Stress Induced Senescence / postreplication repair / SUMOylation of chromatin organization proteins / positive regulation of transcription by RNA polymerase I / mitotic spindle assembly checkpoint signaling / RNA Polymerase I Promoter Escape / nucleolar large rRNA transcription by RNA polymerase I / mitotic sister chromatid segregation / rRNA transcription / Estrogen-dependent gene expression / DNA replication initiation / localization / Ub-specific processing proteases / protein localization to CENP-A containing chromatin / CENP-A containing nucleosome / heterochromatin organization / nucleosomal DNA binding / mitotic spindle organization / meiotic cell cycle / chromosome segregation / kinetochore / structural constituent of chromatin / nucleosome / nucleosome assembly / chromatin organization / sequence-specific DNA binding / protein heterodimerization activity / cell division / DNA repair / protein-containing complex binding / regulation of DNA-templated transcription / structural molecule activity / negative regulation of transcription by RNA polymerase II / DNA binding / nucleus / cytoplasm Similarity search - Function | ||||||||||||
Biological species | ![]() ![]() ![]() ![]() | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.15 Å | ||||||||||||
![]() | Yan, K. / Yang, J. / Zhang, Z. / McLaughlin, S.H. / Chang, L. / Fasci, D. / Heck, A.J.R. / Barford, D. | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Structure of the inner kinetochore CCAN complex assembled onto a centromeric nucleosome. Authors: Kaige Yan / Jing Yang / Ziguo Zhang / Stephen H McLaughlin / Leifu Chang / Domenico Fasci / Ann E Ehrenhofer-Murray / Albert J R Heck / David Barford / ![]() ![]() ![]() ![]() Abstract: In eukaryotes, accurate chromosome segregation in mitosis and meiosis maintains genome stability and prevents aneuploidy. Kinetochores are large protein complexes that, by assembling onto specialized ...In eukaryotes, accurate chromosome segregation in mitosis and meiosis maintains genome stability and prevents aneuploidy. Kinetochores are large protein complexes that, by assembling onto specialized Cenp-A nucleosomes, function to connect centromeric chromatin to microtubules of the mitotic spindle. Whereas the centromeres of vertebrate chromosomes comprise millions of DNA base pairs and attach to multiple microtubules, the simple point centromeres of budding yeast are connected to individual microtubules. All 16 budding yeast chromosomes assemble complete kinetochores using a single Cenp-A nucleosome (Cenp-A), each of which is perfectly centred on its cognate centromere. The inner and outer kinetochore modules are responsible for interacting with centromeric chromatin and microtubules, respectively. Here we describe the cryo-electron microscopy structure of the Saccharomyces cerevisiae inner kinetochore module, the constitutive centromere associated network (CCAN) complex, assembled onto a Cenp-A nucleosome (CCAN-Cenp-A). The structure explains the interdependency of the constituent subcomplexes of CCAN and shows how the Y-shaped opening of CCAN accommodates Cenp-A to enable specific CCAN subunits to contact the nucleosomal DNA and histone subunits. Interactions with the unwrapped DNA duplex at the two termini of Cenp-A are mediated predominantly by a DNA-binding groove in the Cenp-L-Cenp-N subcomplex. Disruption of these interactions impairs assembly of CCAN onto Cenp-A. Our data indicate a mechanism of Cenp-A nucleosome recognition by CCAN and how CCAN acts as a platform for assembly of the outer kinetochore to link centromeres to the mitotic spindle for chromosome segregation. | ||||||||||||
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Structure visualization
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Structure viewer | Molecule: ![]() ![]() |
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PDBx/mmCIF format | ![]() | 687 KB | Display | ![]() |
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PDB format | ![]() | 528.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 802.7 KB | Display | ![]() |
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Full document | ![]() | 820.9 KB | Display | |
Data in XML | ![]() | 81.2 KB | Display | |
Data in CIF | ![]() | 128.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4579MC ![]() 4580C ![]() 4581C ![]() 4971C ![]() 6qleC ![]() 6qlfC 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
-Inner kinetochore subunit ... , 12 types, 12 molecules CHIKLNOPQUYZ
#1: Protein/peptide | Mass: 2754.279 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: ATCC 204508 / S288c / Gene: MIF2, YKL089W / Cell line (production host): High Five / Production host: ![]() |
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#3: Protein | Mass: 15815.147 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: ATCC 204508 / S288c / Gene: MCM16, YPR046W / Cell line (production host): High Five / Production host: ![]() |
#4: Protein | Mass: 47222.789 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: ATCC 204508 / S288c / Gene: CTF3, CHL3, YLR381W / Cell line (production host): High Five / Production host: ![]() |
#6: Protein | Mass: 14082.116 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: ATCC 204508 / S288c / Gene: MCM22, YJR135C, J2122 / Cell line (production host): High Five / Production host: ![]() |
#7: Protein | Mass: 27644.730 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: ATCC 204508 / S288c / Gene: IML3, MCM19, YBR107C, YBR0836 / Cell line (production host): High Five / Production host: ![]() |
#8: Protein | Mass: 51642.430 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: ATCC 204508 / S288c / Gene: CHL4, CTF17, MCM17, YDR254W, YD9320A.04 / Cell line (production host): High Five / Production host: ![]() |
#9: Protein | Mass: 24746.383 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: ATCC 204508 / S288c / Gene: MCM21, CTF5, YDR318W / Cell line (production host): High Five / Production host: ![]() |
#10: Protein | Mass: 31659.006 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: ATCC 204508 / S288c / Gene: CTF19, MCM18, YPL018W, LPB13W / Cell line (production host): High Five / Production host: ![]() |
#11: Protein | Mass: 27358.393 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: ATCC 204508 / S288c / Gene: OKP1, YGR179C / Cell line (production host): High Five / Production host: ![]() |
#12: Protein | Mass: 22157.994 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: ATCC 204508 / S288c / Gene: AME1, ARP100, YBR211C, YBR1458 / Cell line (production host): High Five / Production host: ![]() |
#13: Protein | Mass: 26875.254 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: ATCC 204508 / S288c / Gene: NKP1, YDR383C / Cell line (production host): High Five / Production host: ![]() |
#14: Protein | Mass: 17631.734 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: ATCC 204508 / S288c / Gene: NKP2, YLR315W / Cell line (production host): High Five / Production host: ![]() |
-DNA chain , 2 types, 2 molecules GJ
#2: DNA chain | Mass: 38030.211 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#5: DNA chain | Mass: 38510.504 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
-Histone H3-like centromeric protein ... , 2 types, 2 molecules ae
#15: Protein | Mass: 10535.404 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: ATCC 204508 / S288c / Gene: CSE4, CSL2, YKL049C, YKL262 / Production host: ![]() ![]() |
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#18: Protein | Mass: 13715.144 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: ATCC 204508 / S288c / Gene: CSE4, CSL2, YKL049C, YKL262 / Production host: ![]() ![]() |
-Protein , 5 types, 6 molecules bfdghi
#16: Protein | Mass: 8897.329 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: ATCC 204508 / S288c / Gene: HHF1, YBR009C, YBR0122, HHF2, YNL030W, N2752 / Production host: ![]() ![]() #17: Protein | | Mass: 10342.754 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: ATCC 204508 / S288c / Gene: HTB2, H2B2, YBL002W, YBL0104 / Production host: ![]() ![]() #19: Protein | | Mass: 11546.386 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: ATCC 204508 / S288c / Gene: HTA1, H2A1, SPT11, YDR225W, YD9934.10 / Production host: ![]() ![]() #20: Protein | | Mass: 10413.832 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: ATCC 204508 / S288c / Gene: HTB1, H2B1, SPT12, YDR224C, YD9934.09C / Production host: ![]() ![]() #21: Protein | | Mass: 11190.911 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: ATCC 204508 / S288c / Gene: HTA1, H2A1, SPT11, YDR225W, YD9934.10 / Production host: ![]() ![]() |
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-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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Buffer solution | pH: 8 | ||||||||||||||||||||||||||||||
Specimen | Conc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||||||||
Vitrification | Cryogen name: ETHANE |
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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: 32 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON III (4k x 4k) |
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Processing
Software | Name: PHENIX / Version: 1.14_3260: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 4.15 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 145783 / Symmetry type: POINT | ||||||||||||||||||||||||
Refinement | Highest resolution: 4.15 Å / Stereochemistry target values: CDL v1.2 | ||||||||||||||||||||||||
Refine LS restraints |
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