+Open data
-Basic information
Entry | Database: PDB / ID: 6qld | ||||||||||||
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Title | Structure of inner kinetochore CCAN-Cenp-A complex | ||||||||||||
Components |
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Keywords | DNA BINDING PROTEIN / inner kinetochore / DNA / nucleosome | ||||||||||||
Function / homology | Function and homology information 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 / meiotic sister chromatid segregation / centromere complex 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 / HDMs demethylate histones / PKMTs methylate histone lysines / Mis6-Sim4 complex / meiotic sister chromatid segregation / centromere complex assembly / 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 / attachment of mitotic spindle microtubules to kinetochore / condensed chromosome, centromeric region / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / protein localization to kinetochore / replication fork protection complex / Oxidative Stress Induced Senescence / RMTs methylate histone arginines / postreplication repair / SUMOylation of chromatin organization proteins / spindle pole body / mitotic spindle assembly checkpoint signaling / positive regulation of transcription by RNA polymerase I / RNA Polymerase I Promoter Escape / nucleolar large rRNA transcription by RNA polymerase I / mitotic sister chromatid segregation / protein localization to CENP-A containing chromatin / Estrogen-dependent gene expression / rRNA transcription / CENP-A containing nucleosome / DNA replication initiation / Ub-specific processing proteases / meiotic cell cycle / nucleosomal DNA binding / mitotic spindle organization / chromosome segregation / heterochromatin formation / kinetochore / structural constituent of chromatin / nucleosome / nucleosome assembly / chromatin organization / peroxisome / mitotic cell cycle / sequence-specific DNA binding / protein heterodimerization activity / cell division / DNA repair / regulation of DNA-templated transcription / protein-containing complex binding / structural molecule activity / negative regulation of transcription by RNA polymerase II / DNA binding / nucleus / cytoplasm Similarity search - Function | ||||||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) Escherichia coli (E. coli) | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.15 Å | ||||||||||||
Authors | Yan, K. / Yang, J. / Zhang, Z. / McLaughlin, S.H. / Chang, L. / Fasci, D. / Heck, A.J.R. / Barford, D. | ||||||||||||
Funding support | United Kingdom, 3items
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Citation | Journal: Nature / Year: 2019 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. | ||||||||||||
History |
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-Structure visualization
Movie |
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Structure viewer | Molecule: MolmilJmol/JSmol |
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PDBx/mmCIF format | 6qld.cif.gz | 687 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6qld.ent.gz | 528.6 KB | Display | PDB format |
PDBx/mmJSON format | 6qld.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6qld_validation.pdf.gz | 802.7 KB | Display | wwPDB validaton report |
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Full document | 6qld_full_validation.pdf.gz | 820.9 KB | Display | |
Data in XML | 6qld_validation.xml.gz | 81.2 KB | Display | |
Data in CIF | 6qld_validation.cif.gz | 128.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ql/6qld ftp://data.pdbj.org/pub/pdb/validation_reports/ql/6qld | 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 (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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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.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / Gene: MIF2, YKL089W / Cell line (production host): High Five / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P35201 |
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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.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / Gene: MCM16, YPR046W / Cell line (production host): High Five / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q12262 |
#4: Protein | Mass: 47222.789 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / Gene: CTF3, CHL3, YLR381W / Cell line (production host): High Five / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q12748 |
#6: Protein | Mass: 14082.116 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / Gene: MCM22, YJR135C, J2122 / Cell line (production host): High Five / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P47167 |
#7: Protein | Mass: 27644.730 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / Gene: IML3, MCM19, YBR107C, YBR0836 / Cell line (production host): High Five / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P38265 |
#8: Protein | Mass: 51642.430 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / Gene: CHL4, CTF17, MCM17, YDR254W, YD9320A.04 / Cell line (production host): High Five / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P38907 |
#9: Protein | Mass: 24746.383 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / Gene: MCM21, CTF5, YDR318W / Cell line (production host): High Five / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q06675 |
#10: Protein | Mass: 31659.006 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / Gene: CTF19, MCM18, YPL018W, LPB13W / Cell line (production host): High Five / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q02732 |
#11: Protein | Mass: 27358.393 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / Gene: OKP1, YGR179C / Cell line (production host): High Five / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P53298 |
#12: Protein | Mass: 22157.994 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / Gene: AME1, ARP100, YBR211C, YBR1458 / Cell line (production host): High Five / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P38313 |
#13: Protein | Mass: 26875.254 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / Gene: NKP1, YDR383C / Cell line (production host): High Five / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q12493 |
#14: Protein | Mass: 17631.734 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / Gene: NKP2, YLR315W / Cell line (production host): High Five / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q06162 |
-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.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) |
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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.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) |
-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.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / Gene: CSE4, CSL2, YKL049C, YKL262 / Production host: Escherichia coli (E. coli) / References: UniProt: P36012 |
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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.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / Gene: CSE4, CSL2, YKL049C, YKL262 / Production host: Escherichia coli (E. coli) / References: UniProt: P36012 |
-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.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / Gene: HHF1, YBR009C, YBR0122, HHF2, YNL030W, N2752 / Production host: Escherichia coli (E. coli) / References: UniProt: P02309 #17: Protein | | Mass: 10342.754 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / Gene: HTB2, H2B2, YBL002W, YBL0104 / Production host: Escherichia coli (E. coli) / References: UniProt: P02294 #19: Protein | | Mass: 11546.386 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / Gene: HTA1, H2A1, SPT11, YDR225W, YD9934.10 / Production host: Escherichia coli (E. coli) / References: UniProt: P04911 #20: Protein | | Mass: 10413.832 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / Gene: HTB1, H2B1, SPT12, YDR224C, YD9934.09C / Production host: Escherichia coli (E. coli) / References: UniProt: P02293 #21: Protein | | Mass: 11190.911 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / Gene: HTA1, H2A1, SPT11, YDR225W, YD9934.10 / Production host: Escherichia coli (E. coli) / References: UniProt: P04911 |
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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 |
-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 |
-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: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
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) |
-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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