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- PDB-8ow0: Cryo-EM structure of CBF1-CCAN bound topologically to a centromer... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8ow0 | |||||||||||||||
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Title | Cryo-EM structure of CBF1-CCAN bound topologically to a centromeric CENP-A nucleosome | |||||||||||||||
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Function / homology | ![]() 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 / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | |||||||||||||||
Biological species | ![]() ![]() ![]() | |||||||||||||||
Method | ![]() ![]() ![]() | |||||||||||||||
![]() | Dendooven, T.D. / Zhang, Z. / Yang, J. / McLaughlin, S. / Schwabb, J. / Scheres, S. / Yatskevich, S. / Barford, D. | |||||||||||||||
Funding support | ![]() ![]()
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![]() | ![]() 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
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 1.5 MB | Display | ![]() |
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PDB format | ![]() | 1.3 MB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 17226MC ![]() 8ovwC ![]() 8ovxC ![]() 8ow1C M: map data used to model this data C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Components
-DNA chain , 2 types, 2 molecules DE
#1: DNA chain | Mass: 47239.277 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() ![]() ![]() |
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#2: DNA chain | Mass: 47194.199 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() ![]() ![]() |
-Protein , 5 types, 10 molecules bfdheagcAB
#3: Protein | ![]() Mass: 11395.390 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() Gene: HHF1, YBR009C, YBR0122, HHF2, YNL030W, N2752 / Production host: ![]() ![]() ![]() #4: Protein | Mass: 14280.362 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() Gene: HTB1, H2B1, SPT12, YDR224C, YD9934.09C / Production host: ![]() ![]() ![]() #5: Protein | Mass: 26885.434 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() Gene: CSE4, CSL2, YKL049C, YKL262 / Production host: ![]() ![]() ![]() #6: Protein | Mass: 14013.177 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() Gene: HTA1, H2A1, SPT11, YDR225W, YD9934.10 / Production host: ![]() ![]() ![]() #7: Protein | Mass: 39444.715 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() Gene: CBF1, CEP1, CP1, CPF1, YJR060W, J1730 / Production host: ![]() ![]() |
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-Inner kinetochore subunit ... , 13 types, 13 molecules HIKLNOPQTUWYZ
#8: Protein | Mass: 21166.100 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() Gene: MCM16, YPR046W / Production host: ![]() ![]() |
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#9: Protein | Mass: 84345.633 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() Gene: CTF3, CHL3, YLR381W / Production host: ![]() ![]() |
#10: Protein | Mass: 27602.541 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() Gene: MCM22, YJR135C, J2122 / Production host: ![]() ![]() |
#11: Protein | Mass: 28093.223 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() Gene: IML3, MCM19, YBR107C, YBR0836 / Production host: ![]() ![]() |
#12: Protein | Mass: 52743.723 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() Gene: CHL4, CTF17, MCM17, YDR254W, YD9320A.04 / Production host: ![]() ![]() |
#13: Protein | Mass: 43028.879 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() Gene: MCM21, CTF5, YDR318W / Production host: ![]() ![]() |
#14: Protein | Mass: 42841.113 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() Gene: CTF19, MCM18, YPL018W, LPB13W / Production host: ![]() ![]() |
#15: Protein | Mass: 47427.246 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() Gene: OKP1, YGR179C / Production host: ![]() ![]() |
#16: Protein | Mass: 41359.785 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() Gene: CNN1, YFR046C / Production host: ![]() ![]() |
#17: Protein | Mass: 37506.723 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() Gene: AME1, ARP100, YBR211C, YBR1458 / Production host: ![]() ![]() |
#18: Protein | Mass: 10255.458 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() Gene: WIP1, YDR374W-A / Production host: ![]() ![]() |
#19: Protein | Mass: 27006.451 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() Gene: NKP1, YDR383C / Production host: ![]() ![]() |
#20: Protein | Mass: 17877.033 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() Gene: NKP2, YLR315W / Production host: ![]() ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: ![]() |
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Sample preparation
Component | Name: A complex of CBF1-CCAN bound to centromeric C0N3 DNA / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: ![]() ![]() ![]() |
Source (recombinant) | Organism: ![]() ![]() |
Buffer solution | pH: 8 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied![]() ![]() |
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: 40 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
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Processing
Software | Name: PHENIX / Version: 1.18.2_3874: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction![]() | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction![]() | Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 100311 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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