[English] 日本語
Yorodumi
- EMDB-0051: Core Centromere Binding Factor 3 (CBF3) with monomeric Ndc10 -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: EMDB / ID: 0051
TitleCore Centromere Binding Factor 3 (CBF3) with monomeric Ndc10
Map dataReconstruction of the CBF3CCdeltaN (Core complex of CBF3 comprising the homodimer of Cep3deltaN and the heterodimer of Skp1-Ctf13) in complex with domains 1-2 of Ndc10
SampleCore CBF3 in complex with Ndc10 D1-2
  • (Centromere DNA-binding protein complex CBF3 subunit ...) x 3
  • Suppressor of kinetochore protein 1
Function / homologyS-phase kinase-associated protein 1-like / Skp1 family, dimerisation domain / Integrase/recombinase, N-terminal / SKP1/BTB/POZ domain superfamily / SKP1 component, dimerisation / SKP1 component, POZ domain / S-phase kinase-associated protein 1 / Transcription activator GCR1-like domain / Centromere DNA-binding protein complex CBF3 subunit B, C-terminal / Ndc10, domain 2 ...S-phase kinase-associated protein 1-like / Skp1 family, dimerisation domain / Integrase/recombinase, N-terminal / SKP1/BTB/POZ domain superfamily / SKP1 component, dimerisation / SKP1 component, POZ domain / S-phase kinase-associated protein 1 / Transcription activator GCR1-like domain / Centromere DNA-binding protein complex CBF3 subunit B, C-terminal / Ndc10, domain 2 / Leucine-rich repeat domain superfamily / SKP1-like, dimerisation domain superfamily / Zn(2)-C6 fungal-type DNA-binding domain superfamily / Ndc10, domain 2 superfamily / Zn(2)-C6 fungal-type DNA-binding domain / Fungal Zn(2)-Cys(6) binuclear cluster domain / Skp1 family, tetramerisation domain / Transcriptional activator of glycolytic enzymes / Antigen processing: Ubiquitination & Proteasome degradation / Iron uptake and transport / Neddylation / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / Orc1 removal from chromatin / SCF(Skp2)-mediated degradation of p27/p21 / SCF-beta-TrCP mediated degradation of Emi1 / Zn(2)-C6 fungal-type DNA-binding domain profile. / Zn(2)-C6 fungal-type DNA-binding domain signature. / Centromere DNA-binding protein complex CBF3 subunit B / Centromere DNA-binding protein complex CBF3 subunit, domain 2 / RAVE complex / CBF3 complex / septin ring assembly / centromeric DNA binding / mitotic spindle elongation / exit from mitosis / negative regulation of cytoplasmic translation / vacuolar acidification / kinetochore assembly / condensed nuclear chromosome kinetochore / protein neddylation / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / regulation of exit from mitosis / SCF ubiquitin ligase complex / spindle pole body / DNA binding, bending / DNA replication origin binding / cellular protein-containing complex assembly / condensed nuclear chromosome, centromeric region / mitotic spindle assembly checkpoint / condensed chromosome kinetochore / regulation of protein complex assembly / spindle midzone / kinetochore / chromosome segregation / spindle / G1/S transition of mitotic cell cycle / ubiquitin-dependent protein catabolic process / G2/M transition of mitotic cell cycle / protein ubiquitination / DNA-binding transcription factor activity, RNA polymerase II-specific / zinc ion binding / identical protein binding / nucleus / cytoplasm / Centromere DNA-binding protein complex CBF3 subunit A / Centromere DNA-binding protein complex CBF3 subunit C / Centromere DNA-binding protein complex CBF3 subunit B / Suppressor of kinetochore protein 1
Function and homology information
SourceSaccharomyces cerevisiae (baker's yeast)
Methodsingle particle reconstruction / cryo EM / 4.2 Å resolution
AuthorsZhang WJ / Lukoynova N / Vaughan CK
CitationJournal: 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 Lukoynova / 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.
Validation ReportPDB-ID: 6gsa

SummaryFull reportAbout validation report
DateDeposition: Jun 13, 2018 / Header (metadata) release: Jul 4, 2018 / Map release: Aug 1, 2018 / Last update: Aug 1, 2018

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0174
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.0174
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-6gsa
  • Surface level: 0.0174
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

-
Map

Fileemd_0051.map.gz (map file in CCP4 format, 67109 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
256 pix
1.06 Å/pix.
= 271.36 Å
256 pix
1.06 Å/pix.
= 271.36 Å
256 pix
1.06 Å/pix.
= 271.36 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
Density
Contour Level:0.0174 (by author), 0.0174 (movie #1):
Minimum - Maximum-0.02745911 - 0.09228461
Average (Standard dev.)0.00013709656 (0.0042895144)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions256256256
Origin0.0.0.
Limit255.255.255.
Spacing256256256
CellA=B=C: 271.36 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.061.061.06
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z271.360271.360271.360
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.0270.0920.000

-
Supplemental data

-
Sample components

+
Entire Core CBF3 in complex with Ndc10 D1-2

EntireName: Core CBF3 in complex with Ndc10 D1-2
Details: The truncated CBF3 complex, recombinantly expressed in Saccharomyces cerevisiae. It comprises a Cep3 homodimer, in which the binuclear zinc cluster domains are truncated, full length heterodimer of Skp1 and Ctf13, and a monomeric construct Ndc10 comprising domains 1-2.
Number of components: 5

+
Component #1: protein, Core CBF3 in complex with Ndc10 D1-2

ProteinName: Core CBF3 in complex with Ndc10 D1-2
Details: The truncated CBF3 complex, recombinantly expressed in Saccharomyces cerevisiae. It comprises a Cep3 homodimer, in which the binuclear zinc cluster domains are truncated, full length heterodimer of Skp1 and Ctf13, and a monomeric construct Ndc10 comprising domains 1-2.
Recombinant expression: No
MassTheoretical: 286 kDa
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)
Source (engineered)Expression System: Saccharomyces cerevisiae (baker's yeast) / Vector: modified pRS424 and pRS426

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

ProteinName: Centromere DNA-binding protein complex CBF3 subunit B
Details: N-terminal polyhistidine purification tagTruncation of the binuclear zinc cluster domain
Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 68.454125 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: 22.558451 kDa
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)
Source (engineered)Expression System: Saccharomyces cerevisiae (baker's yeast)

+
Component #4: protein, Centromere DNA-binding protein complex CBF3 subunit C

ProteinName: Centromere DNA-binding protein complex CBF3 subunit C / Details: C-terminal CBP purification tag / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 60.899961 kDa
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)
Source (engineered)Expression System: Saccharomyces cerevisiae (baker's yeast)

+
Component #5: protein, Centromere DNA-binding protein complex CBF3 subunit A

ProteinName: Centromere DNA-binding protein complex CBF3 subunit A
Details: Domains 1-2 of Ndc10 with a non-cleavable C-terminal StrepII tag
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 66.159578 kDa
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)
Source (engineered)Expression System: Saccharomyces cerevisiae (baker's yeast)

-
Experimental details

-
Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionSpecimen conc.: 0.15 mg/ml / pH: 8
VitrificationInstrument: FEI VITROBOT MARK I / Cryogen name: ETHANE / Temperature: 277 K / Humidity: 100 %

-
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: 5 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 47170. X (calibrated) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

-
Image acquisition

Image acquisitionNumber of digital images: 2003

-
Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 56509
Details: The selected images were high-pass filtered and normalized.
3D reconstructionAlgorithm: FOURIER SPACE / Resolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot
(resolution estimation)

-
Atomic model buiding

Modeling #1Details: "Fit in map" function used to place 6FE8 and 4ACO with out further refinement or model building
Output model

+
About Yorodumi

-
News

-
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. See below links for details.
  • 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

+
Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi

+
Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi

+
Apr 13, 2016. Omokage search got faster

Omokage search got faster

  • The computation time became ~1/2 compared to the previous version by re-optimization of data accession
  • Enjoy "shape similarity" of biomolecules, more!

Related info.: Omokage search

Read more

-
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.

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