[English] 日本語
Yorodumi
- EMDB-4163: CBF3 Core Complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-4163
TitleCBF3 Core Complex
Map data
SampleCBF3 Core Complex
  • Centromere DNA-binding protein complex CBF3 subunit B
  • Suppressor of kinetochore protein 1
  • ligand
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 / SKP1-like, dimerisation domain superfamily / S-phase kinase-associated protein 1 ...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 / SKP1-like, dimerisation domain superfamily / S-phase kinase-associated protein 1 / SKP1 component, dimerisation / Skp1 family, dimerisation domain / Skp1 family, tetramerisation domain / SKP1 component, POZ domain / Found in Skp1 protein family / S-phase kinase-associated protein 1-like / 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 (baker'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
Wellcome TrustFC001155 United Kingdom
Medical Research Council (United Kingdom)FC001155 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-
UpdateDec 11, 2019-
Current statusDec 11, 2019Processing site: PDBe / Status: Released

-
Structure visualization

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

Downloads & links

-
Map

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

-
Supplemental data

-
Sample components

-
Entire CBF3 Core Complex

EntireName: CBF3 Core Complex / Number of Components: 4

-
Component #1: protein, CBF3 Core Complex

ProteinName: CBF3 Core Complex / Recombinant expression: No
MassTheoretical: 220 kDa
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)
Source (engineered)Expression System: Saccharomyces cerevisiae (baker's yeast)

-
Component #2: protein, Centromere DNA-binding protein complex CBF3 subunit B

ProteinName: Centromere DNA-binding protein complex CBF3 subunit B / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 72.637117 kDa
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)
Source (engineered)Expression System: Saccharomyces cerevisiae (baker's yeast)

-
Component #3: protein, Suppressor of kinetochore protein 1

ProteinName: Suppressor of kinetochore protein 1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 22.35727 kDa
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)
Source (engineered)Expression System: Saccharomyces cerevisiae (baker's yeast)

-
Component #4: ligand, ZINC ION

LigandName: ZINC ION / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 6.540905 MDa

-
Experimental details

-
Sample preparation

SpecimenSpecimen State: Particle / Method: cryo EM
Sample solutionpH: 7.5
VitrificationCryogen Name: ETHANE

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron Source: FIELD EMISSION GUN / Accelerating Voltage: 300 kV / Electron Dose: 2.16 e/Å2 / Illumination Mode: FLOOD BEAM
LensImaging Mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

-
Image processing

ProcessingMethod: single particle reconstruction / Applied Symmetry: C1 (asymmetric) / Number of Projections: 209751
3D reconstructionSoftware: RELION / Resolution: 3.6 Å / Resolution Method: FSC 0.143 CUT-OFF
FSC plot (resolution estimation)

-
Atomic model buiding

Output model

+
About Yorodumi

-
News

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

-
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242):Coronavirus Proteases

+
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

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

+
Jun 16, 2017. Omokage search with filter

Omokage search with filter

Result of Omokage search can be filtered by keywords and the database types

Related info.:Omokage search

-
Yorodumi

Thousand views of thousand structures

  • 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

Read more