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Open data
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Basic information
Entry | Database: PDB / ID: 7k79 | ||||||
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Title | CBF3 | ||||||
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Function / homology | ![]() RAVE complex / Iron uptake and transport / CBF3 complex / regulation of transcription by galactose / regulation of sulfur amino acid metabolic process / cellular response to methylmercury / vacuolar proton-transporting V-type ATPase complex assembly / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
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Method | ![]() ![]() ![]() | ||||||
![]() | Ruifang, G. / Yawen, B. | ||||||
![]() | ![]() Title: Structural and dynamic mechanisms of CBF3-guided centromeric nucleosome formation. Authors: Ruifang Guan / Tengfei Lian / Bing-Rui Zhou / Emily He / Carl Wu / Martin Singleton / Yawen Bai / ![]() ![]() Abstract: Accurate chromosome segregation relies on the specific centromeric nucleosome-kinetochore interface. In budding yeast, the centromere CBF3 complex guides the deposition of CENP-A, an H3 variant, to ...Accurate chromosome segregation relies on the specific centromeric nucleosome-kinetochore interface. In budding yeast, the centromere CBF3 complex guides the deposition of CENP-A, an H3 variant, to form the centromeric nucleosome in a DNA sequence-dependent manner. Here, we determine the structures of the centromeric nucleosome containing the native CEN3 DNA and the CBF3core bound to the canonical nucleosome containing an engineered CEN3 DNA. The centromeric nucleosome core structure contains 115 base pair DNA including a CCG motif. The CBF3core specifically recognizes the nucleosomal CCG motif through the Gal4 domain while allosterically altering the DNA conformation. Cryo-EM, modeling, and mutational studies reveal that the CBF3core forms dynamic interactions with core histones H2B and CENP-A in the CEN3 nucleosome. Our results provide insights into the structure of the budding yeast centromeric nucleosome and the mechanism of its assembly, which have implications for analogous processes of human centromeric nucleosome formation. | ||||||
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Structure visualization
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Structure viewer | Molecule: ![]() ![]() |
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PDBx/mmCIF format | ![]() | 297.4 KB | Display | ![]() |
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PDB format | ![]() | 246.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 22697MC ![]() 7k78C ![]() 7k7gC M: map data used to model this data C: citing same article ( |
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Similar structure data |
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Assembly
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Components
#1: Protein | Mass: 60899.961 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() Strain: ATCC 204508 / S288c / Gene: CTF13, CBF3C, YMR094W, YM6543.01, YM9582.19 / Production host: ![]() ![]() ![]() | ||
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#2: Protein | Mass: 72637.117 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() Strain: ATCC 204508 / S288c / Gene: CEP3, CBF3, CBF3B, CSL1, YMR168C, YM8520.17C / Production host: ![]() ![]() ![]() #3: Protein | | Mass: 22357.270 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() Strain: ATCC 204508 / S288c / Gene: SKP1, CBF3D, YDR328C, D9798.14 / 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: CBF3CORE / Type: COMPLEX / Entity ID: #1-#2 / Source: NATURAL |
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Source (natural) | Organism: ![]() ![]() ![]() |
Buffer solution | pH: 7.3 |
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: 71 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
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Processing
CTF correction![]() | Type: NONE |
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3D reconstruction![]() | Resolution: 4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 115666 / Symmetry type: POINT |