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- PDB-7k79: CBF3 -

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Basic information

Entry
Database: PDB / ID: 7k79
TitleCBF3
Components
  • Centromere DNA-binding protein complex CBF3 subunit B
  • Centromere DNA-binding protein complex CBF3 subunit C
  • Suppressor of kinetochore protein 1
KeywordsDNA BINDING PROTEIN / CBF3
Function / homology
Function and homology information


RAVE complex / CBF3 complex / Neddylation / septin ring assembly / negative regulation of cytoplasmic translation / centromeric DNA binding / vacuolar acidification / regulation of exit from mitosis / kinetochore assembly / exit from mitosis ...RAVE complex / CBF3 complex / Neddylation / septin ring assembly / negative regulation of cytoplasmic translation / centromeric DNA binding / vacuolar acidification / regulation of exit from mitosis / kinetochore assembly / exit from mitosis / protein neddylation / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / SCF ubiquitin ligase complex / DNA binding, bending / cullin family protein binding / mitotic spindle assembly checkpoint signaling / protein-containing complex assembly => GO:0065003 / DNA replication origin binding / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / : / Orc1 removal from chromatin / Antigen processing: Ubiquitination & Proteasome degradation / regulation of protein-containing complex assembly / kinetochore / G1/S transition of mitotic cell cycle / G2/M transition of mitotic cell cycle / ubiquitin-dependent protein catabolic process / mitotic cell cycle / protein ubiquitination / DNA-binding transcription factor activity, RNA polymerase II-specific / zinc ion binding / identical protein binding / nucleus / cytoplasm
Similarity search - Function
Centromere DNA-binding protein complex CBF3 subunit B, C-terminal / Centromere DNA-binding protein complex CBF3 subunit B / Zn(2)-C6 fungal-type DNA-binding domain signature. / Fungal Zn(2)-Cys(6) binuclear cluster domain / Zn(2)-C6 fungal-type DNA-binding domain profile. / GAL4-like Zn(II)2Cys6 (or C6 zinc) binuclear cluster DNA-binding domain / Zn(2)-C6 fungal-type DNA-binding domain superfamily / Zn(2)-C6 fungal-type DNA-binding domain / S-phase kinase-associated protein 1 / SKP1-like, dimerisation domain superfamily ...Centromere DNA-binding protein complex CBF3 subunit B, C-terminal / Centromere DNA-binding protein complex CBF3 subunit B / Zn(2)-C6 fungal-type DNA-binding domain signature. / Fungal Zn(2)-Cys(6) binuclear cluster domain / Zn(2)-C6 fungal-type DNA-binding domain profile. / GAL4-like Zn(II)2Cys6 (or C6 zinc) binuclear cluster DNA-binding domain / Zn(2)-C6 fungal-type DNA-binding domain superfamily / Zn(2)-C6 fungal-type DNA-binding domain / S-phase kinase-associated protein 1 / SKP1-like, dimerisation domain superfamily / Skp1 family, dimerisation domain / SKP1 component, dimerisation / SKP1 component, POZ domain / S-phase kinase-associated protein 1-like / Found in Skp1 protein family / Skp1 family, tetramerisation domain / SKP1/BTB/POZ domain superfamily / Leucine-rich repeat domain superfamily
Similarity search - Domain/homology
Centromere DNA-binding protein complex CBF3 subunit C / Centromere DNA-binding protein complex CBF3 subunit B / Suppressor of kinetochore protein 1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (baker's yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4 Å
AuthorsRuifang, G. / Yawen, B.
CitationJournal: Nat Commun / Year: 2021
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.
History
DepositionSep 22, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 31, 2021Provider: repository / Type: Initial release

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Assembly

Deposited unit
K: Centromere DNA-binding protein complex CBF3 subunit C
L: Centromere DNA-binding protein complex CBF3 subunit B
O: Centromere DNA-binding protein complex CBF3 subunit B
N: Suppressor of kinetochore protein 1


Theoretical massNumber of molelcules
Total (without water)228,5314
Polymers228,5314
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Centromere DNA-binding protein complex CBF3 subunit C / Chromosome transmission fidelity protein 13 / Kinetochore protein CTF13


Mass: 60899.961 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: CTF13, CBF3C, YMR094W, YM6543.01, YM9582.19 / Production host: Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P35203
#2: Protein Centromere DNA-binding protein complex CBF3 subunit B / Centromere protein 3


Mass: 72637.117 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: CEP3, CBF3, CBF3B, CSL1, YMR168C, YM8520.17C / Production host: Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P40969
#3: Protein Suppressor of kinetochore protein 1 / Centromere DNA-binding protein complex CBF3 subunit D / E3 ubiquitin ligase complex SCF subunit SKP1


Mass: 22357.270 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: SKP1, CBF3D, YDR328C, D9798.14 / Production host: Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P52286

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: CBF3CORE / Type: COMPLEX / Entity ID: #1-#2 / Source: NATURAL
Source (natural)Organism: Saccharomyces cerevisiae (baker's yeast)
Buffer solutionpH: 7.3
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 71 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

CTF correctionType: NONE
3D reconstructionResolution: 4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 115666 / Symmetry type: POINT

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