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- EMDB-4163: CBF3 Core Complex -

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Basic information

Entry
Database: EMDB / ID: EMD-4163
TitleCBF3 Core Complex
Map dataCBF3 core
Sample
  • Complex: CBF3 Core Complex
    • Protein or peptide: Centromere DNA-binding protein complex CBF3 subunit B
    • Protein or peptide: Suppressor of kinetochore protein 1
  • Ligand: ZINC ION
Keywordskinetochore / F-box / DNA-binding / centromere / CELL CYCLE
Function / homology
Function and homology information


RAVE complex / Iron uptake and transport / CBF3 complex / regulation of transcription by galactose / cellular response to methylmercury / vacuolar proton-transporting V-type ATPase complex assembly / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / septin ring assembly / exit from mitosis / centromeric DNA binding ...RAVE complex / Iron uptake and transport / CBF3 complex / regulation of transcription by galactose / cellular response to methylmercury / vacuolar proton-transporting V-type ATPase complex assembly / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / septin ring assembly / exit from mitosis / centromeric DNA binding / regulation of exit from mitosis / Antigen processing: Ubiquitination & Proteasome degradation / positive regulation of D-glucose transmembrane transport / vacuolar acidification / mitotic intra-S DNA damage checkpoint signaling / protein neddylation / mitochondrial fusion / silent mating-type cassette heterochromatin formation / DNA binding, bending / kinetochore assembly / mitotic spindle assembly checkpoint signaling / SCF ubiquitin ligase complex / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / DNA replication origin binding / subtelomeric heterochromatin formation / regulation of protein-containing complex assembly / cullin family protein binding / negative regulation of cytoplasmic translation / endomembrane system / regulation of mitotic cell cycle / G1/S transition of mitotic cell cycle / G2/M transition of mitotic cell cycle / kinetochore / mitotic cell cycle / protein-containing complex assembly / ubiquitin-dependent protein catabolic process / DNA-binding transcription factor activity, RNA polymerase II-specific / chromosome, telomeric region / protein ubiquitination / 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 superfamily / 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 / SKP1 component, dimerisation / S-phase kinase-associated protein 1 ...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 superfamily / 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 / SKP1 component, dimerisation / S-phase kinase-associated protein 1 / SKP1-like, dimerisation domain superfamily / Skp1 family, dimerisation domain / S-phase kinase-associated protein 1-like / SKP1 component, POZ domain / Skp1 family, tetramerisation domain / Found in Skp1 protein family / SKP1/BTB/POZ domain superfamily
Similarity search - Domain/homology
Centromere DNA-binding protein complex CBF3 subunit B / Suppressor of kinetochore protein 1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsLeber V / Singleton MR
Funding support United Kingdom, 3 items
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, 2017-
Header (metadata) releaseDec 13, 2017-
Map releaseDec 13, 2017-
UpdateOct 9, 2024-
Current statusOct 9, 2024Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.055
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.055
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6f07
  • Surface level: 0.055
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6f07
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_4163.png

Downloads & links

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Map

FileDownload / File: emd_4163.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCBF3 core
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 240 pix.
= 258.72 Å		1.08 Å/pix.
x 240 pix.
= 258.72 Å		1.08 Å/pix.
x 240 pix.
= 258.72 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.078 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.055 / Movie #1: 0.055
Minimum - Maximum-0.21864027 - 0.33394143
Average (Standard dev.)0.00037990836 (±0.009680248)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 258.72 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0781.0781.078
M x/y/z240240240
origin x/y/z0.0000.0000.000
length x/y/z258.720258.720258.720
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS240240240
D min/max/mean-0.2190.3340.000

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Supplemental data

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Sample components

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Entire : CBF3 Core Complex

EntireName: CBF3 Core Complex
Components
  • Complex: CBF3 Core Complex
    • Protein or peptide: Centromere DNA-binding protein complex CBF3 subunit B
    • Protein or peptide: Suppressor of kinetochore protein 1
  • Ligand: ZINC ION

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Supramolecule #1: CBF3 Core Complex

SupramoleculeName: CBF3 Core Complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 220 KDa

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Macromolecule #1: Centromere DNA-binding protein complex CBF3 subunit B

MacromoleculeName: Centromere DNA-binding protein complex CBF3 subunit B / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 72.637117 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MFNRTTQLKS KHPCSVCTRR KVKCDRMIPC GNCRKRGQDS ECMKSTKLIT ASSSKEYLPD LLLFWQNYEY WITNIGLYKT KQRDLTRTP ANLDTDTEEC MFWMNYLQKD QSFQLMNFAM ENLGALYFGS IGDISELYLR VEQYWDRRAD KNHSVDGKYW D ALIWSVFT ...String:
MFNRTTQLKS KHPCSVCTRR KVKCDRMIPC GNCRKRGQDS ECMKSTKLIT ASSSKEYLPD LLLFWQNYEY WITNIGLYKT KQRDLTRTP ANLDTDTEEC MFWMNYLQKD QSFQLMNFAM ENLGALYFGS IGDISELYLR VEQYWDRRAD KNHSVDGKYW D ALIWSVFT MCIYYMPVEK LAEIFSVYPL HEYLGSNKRL NWEDGMQLVM CQNFARCSLF QLKQCDFMAH PDIRLVQAYL IL ATTTFPY DEPLLANSLL TQCIHTFKNF HVDDFRPLLN DDPVESIAKV TLGRIFYRLC GCDYLQSGPR KPIALHTEVS SLL QHAAYL QDLPNVDVYR EENSTEVLYW KIISLDRDLD QYLNKSSKPP LKTLDAIRRE LDIFQYKVDS LEEDFRSNNS RFQK FIALF QISTVSWKLF KMYLIYYDTA DSLLKVIHYS KVIISLIVNN FHAKSEFFNR HPMVMQTITR VVSFISFYQI FVESA AVKQ LLVDLTELTA NLPTIFGSKL DKLVYLTERL SKLKLLWDKV QLLDSGDSFY HPVFKILQND IKIIELKNDE MFSLIK GLG SLVPLNKLRQ ESLLEEEDEN NTEPSDFRTI VEEFQSEYNI SDILSGSGGS GENLYFQ

UniProtKB: Centromere DNA-binding protein complex CBF3 subunit B

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Macromolecule #2: Suppressor of kinetochore protein 1

MacromoleculeName: Suppressor of kinetochore protein 1 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 22.35727 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MVTSNVVLVS GEGERFTVDK KIAERSLLLK NYLNDMHDSN LQNNSDSESD SDSETNHKSK DNNNGDDDDE DDDEIVMPVP NVRSSVLQK VIEWAEHHRD SNFPDEDDDD SRKSAPVDSW DREFLKVDQE MLYEIILAAN YLNIKPLLDA GCKVVAEMIR G RSPEEIRR ...String:
MVTSNVVLVS GEGERFTVDK KIAERSLLLK NYLNDMHDSN LQNNSDSESD SDSETNHKSK DNNNGDDDDE DDDEIVMPVP NVRSSVLQK VIEWAEHHRD SNFPDEDDDD SRKSAPVDSW DREFLKVDQE MLYEIILAAN YLNIKPLLDA GCKVVAEMIR G RSPEEIRR TFNIVNDFTP EEEAAIRREN EWAEDR

UniProtKB: Suppressor of kinetochore protein 1

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Macromolecule #3: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 3 / Number of copies: 2 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 2.16 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

2veq

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.1.1) / Number images used: 209751
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementProtocol: OTHER
Output model

PDB-6f07:
CBF3 Core Complex

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