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- PDB-6f07: CBF3 Core Complex -

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Basic information

Entry
Database: PDB / ID: 6f07
TitleCBF3 Core Complex
Components
  • Centromere DNA-binding protein complex CBF3 subunit B
  • Suppressor of kinetochore protein 1
KeywordsCELL CYCLE / kinetochore / F-box / DNA-binding / centromere
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 / Centromere DNA-binding protein complex CBF3 subunit B, C-terminal / 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. / Zn(2)-C6 fungal-type DNA-binding domain superfamily / GAL4-like Zn(II)2Cys6 (or C6 zinc) binuclear cluster DNA-binding domain / Zn(2)-C6 fungal-type DNA-binding domain / S-phase kinase-associated protein 1 / SKP1 component, dimerisation ...Centromere DNA-binding protein complex CBF3 subunit B / Centromere DNA-binding protein complex CBF3 subunit B, C-terminal / 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. / Zn(2)-C6 fungal-type DNA-binding domain superfamily / GAL4-like Zn(II)2Cys6 (or C6 zinc) binuclear cluster DNA-binding domain / Zn(2)-C6 fungal-type DNA-binding domain / S-phase kinase-associated protein 1 / SKP1 component, dimerisation / Skp1 family, dimerisation domain / SKP1-like, dimerisation domain superfamily / Skp1 family, tetramerisation domain / SKP1 component, POZ domain / Found in Skp1 protein family / S-phase kinase-associated protein 1-like / Potassium Channel Kv1.1; Chain A / Potassium Channel Kv1.1; Chain A / SKP1/BTB/POZ domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
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: 3.6 Å
AuthorsLeber, V. / Singleton, M.R.
Funding support United Kingdom, 3items
OrganizationGrant numberCountry
Cancer Research UKFC001155 United Kingdom
Medical Research Council (United Kingdom)FC001155 United Kingdom
Wellcome TrustFC001155 United Kingdom
CitationJournal: EMBO J / Year: 2018
Title: Structural basis for assembly of the CBF3 kinetochore complex.
Authors: Vera Leber / Andrea Nans / Martin R Singleton /
Abstract: Eukaryotic chromosomes contain a specialised region known as the centromere, which forms the platform for kinetochore assembly and microtubule attachment. The centromere is distinguished by the ...Eukaryotic chromosomes contain a specialised region known as the centromere, which forms the platform for kinetochore assembly and microtubule attachment. The centromere is distinguished by the presence of nucleosomes containing the histone H3 variant, CENP-A. In budding yeast, centromere establishment begins with the recognition of a specific DNA sequence by the CBF3 complex. This in turn facilitates CENP-A nucleosome deposition and kinetochore assembly. Here, we describe a 3.6 Å single-particle cryo-EM reconstruction of the core CBF3 complex, incorporating the sequence-specific DNA-binding protein Cep3 together with regulatory subunits Ctf13 and Skp1. This provides the first structural data on Ctf13, defining it as an F-box protein of the leucine-rich-repeat family, and demonstrates how a novel F-box-mediated interaction between Ctf13 and Skp1 is responsible for initial assembly of the CBF3 complex.
History
DepositionNov 17, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 13, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2017Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 31, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.3Nov 21, 2018Group: Advisory / Data collection / Derived calculations
Category: pdbx_validate_close_contact / struct_conn / struct_conn_type
Revision 1.4Dec 11, 2019Group: Other / Category: atom_sites / cell
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] ..._atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3] / _cell.Z_PDB

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Assembly

Deposited unit
A: Centromere DNA-binding protein complex CBF3 subunit B
B: Centromere DNA-binding protein complex CBF3 subunit B
D: Suppressor of kinetochore protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)167,7625
Polymers167,6323
Non-polymers1312
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area7660 Å2
ΔGint-52 kcal/mol
Surface area59990 Å2
MethodPISA

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Components

#1: 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 (baker's yeast)
Gene: CEP3, CBF3, CBF3B, CSL1, YMR168C, YM8520.17C / Production host: Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P40969
#2: 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 (baker's yeast)
Gene: SKP1, CBF3D, YDR328C, D9798.14 / Production host: Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P52286
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn

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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: CBF3 Core Complex / Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Molecular weightValue: 0.22 MDa / Experimental value: NO
Source (natural)Organism: Saccharomyces cerevisiae (baker's yeast)
Source (recombinant)Organism: Saccharomyces cerevisiae (baker's yeast)
Buffer solutionpH: 7.5
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: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 2.16 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.12_2829: / Classification: refinement
EM software
IDNameVersionCategory
7Coot0.86model fitting
9PHENIX1.12model refinement
13RELION2.1.13D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 209751 / Symmetry type: POINT
Atomic model buildingProtocol: OTHER
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00810385
ELECTRON MICROSCOPYf_angle_d1.04114049
ELECTRON MICROSCOPYf_dihedral_angle_d6.0736251
ELECTRON MICROSCOPYf_chiral_restr0.0581556
ELECTRON MICROSCOPYf_plane_restr0.0081771

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