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 species
Saccharomyces cerevisiae (brewer's yeast)
Method
single particle reconstruction / cryo EM / Resolution: 3.7 Å
Biotechnology and Biological Sciences Research Council
BB/J007595/1
United Kingdom
Citation
Journal: Cell Rep / Year: 2018 Title: Insights into Centromere DNA Bending Revealed by the Cryo-EM Structure of the Core Centromere Binding Factor 3 with Ndc10. Authors: Wenjuan Zhang / Natalya Lukoyanova / Shomon Miah / Jonathan Lucas / Cara K Vaughan / Abstract: The centromere binding factor 3 (CBF3) complex binds the third centromere DNA element in organisms with point centromeres, such as S. cerevisiae. It is an essential complex for assembly of the ...The centromere binding factor 3 (CBF3) complex binds the third centromere DNA element in organisms with point centromeres, such as S. cerevisiae. It is an essential complex for assembly of the kinetochore in these organisms, as it facilitates genetic centromere specification and allows association of all other kinetochore components. We determined high-resolution structures of the core complex of CBF3 alone and in association with a monomeric construct of Ndc10, using cryoelectron microscopy (cryo-EM). We identify the DNA-binding site of the complex and present a model in which CBF3 induces a tight bend in centromeric DNA, thus facilitating assembly of the centromeric nucleosome.
History
Deposition
Dec 30, 2017
-
Header (metadata) release
Jan 10, 2018
-
Map release
Aug 1, 2018
-
Update
Dec 11, 2019
-
Current status
Dec 11, 2019
Processing site: PDBe / Status: Released
-
Structure visualization
Movie
Surface view with section colored by density value
Entire : The core Centromere Binding Factor 3 complex
Entire
Name: The core Centromere Binding Factor 3 complex
Components
Complex: The core Centromere Binding Factor 3 complex
Protein or peptide: Centromere DNA-binding protein complex CBF3 subunit B
Protein or peptide: Suppressor of kinetochore protein 1
Protein or peptide: Centromere DNA-binding protein complex CBF3 subunit C
-
Supramolecule #1: The core Centromere Binding Factor 3 complex
Supramolecule
Name: The core Centromere Binding Factor 3 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all Details: The core CBF3 complex, recombinantly expressed in Saccharomyces cerevisiae. It comprises a Cep3 homodimer, in which the binuclear zinc cluster domains are truncated, and full length Skp1 and Ctf13 components.
Macromolecule #1: Centromere DNA-binding protein complex CBF3 subunit B
Macromolecule
Name: Centromere DNA-binding protein complex CBF3 subunit B / type: protein_or_peptide / ID: 1 / Details: Model is numbered according to / Number of copies: 2 / Enantiomer: LEVO
The selected images were high-pass filtered and normalized.
Particle selection
Number selected: 139303
CTF correction
Software - Name: CTFFIND (ver. 4.0) Software - details: CTF parameters were estimated using CTFFIND4
Startup model
Type of model: OTHER Details: An ovoid generated from SPIDER was used as an initial model for 3D classification.
Final reconstruction
Number classes used: 4 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.0) Details: 3D auto-refinement of all the good particles from 2D classification, provided a reconstruction at 4.7 angstrom overall resolution. After post-process by RELION and sharpened by a negative B- ...Details: 3D auto-refinement of all the good particles from 2D classification, provided a reconstruction at 4.7 angstrom overall resolution. After post-process by RELION and sharpened by a negative B-factor using an automated procedure resulting in a 4.1 angstrom reconstruction. Number images used: 69392
Number classes: 4 / Avg.num./class: 17348 / Software - Name: RELION (ver. 2.0) Details: The automatically picked particles were screened manually followed by reference-free 2D classification, which yielded 69,392 particles for subsequent 3D classification.
FSC plot (resolution estimation)
+
Image processing #2
Image processing ID
2
Image recording ID
2
Details
The selected images were high-pass filtered and normalized.
Particle selection
Number selected: 289281
CTF correction
Software - Name: CTFFIND (ver. 4.0) Software - details: CTF parameters were estimated using CTFFIND4
Startup model
Type of model: OTHER Details: An ovoid generated from SPIDER was used as an initial model for 3D classification.
Final reconstruction
Number classes used: 2 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.0) Details: 187, 606 particles were in the best two 3D classes. 3D auto-refinement of the 3D joined classes against the corresponding particles resulted in a final reconstruction. Number images used: 187606
Number classes: 3 / Avg.num./class: 94038 / Software - Name: RELION (ver. 2.0) Details: After joining the two dataset of selection from 2D classification , 282,116 particles were input to 3D classification using an initial 3D reference obtained by low pass-filtering the ...Details: After joining the two dataset of selection from 2D classification , 282,116 particles were input to 3D classification using an initial 3D reference obtained by low pass-filtering the reconstruction of map from the first dataset, resulting two best 3D classes, which in total contain 67 percent of the whole particles.
In the structure databanks used in Yorodumi, some data are registered as the other names, "COVID-19 virus" and "2019-nCoV". Here are the details of the virus and the list of structure data.
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)
EMDB accession codes are about to change! (news from PDBe EMDB page)
The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
The EM Navigator/Yorodumi systems omit the EMD- prefix.
Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator
Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.
Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi