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- EMDB-0095: Cryo-EM structure of the CBF3-core-Ndc10-DBD complex of the buddi... -

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Basic information

Entry
Database: EMDB / ID: 0095
TitleCryo-EM structure of the CBF3-core-Ndc10-DBD complex of the budding yeast kinetochore
Map dataCBF3-core-Ndc10-DBD
SampleCBF3-core-Ndc10-DBD complex
  • (Centromere DNA-binding protein complex CBF3 subunit ...) x 4
  • Suppressor of kinetochore protein 1
  • (ligand) x 6
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 / Antigen processing: Ubiquitination & Proteasome degradation / Centromere DNA-binding protein complex CBF3 subunit, domain 2 / Centromere DNA-binding protein complex CBF3 subunit B / Zn(2)-C6 fungal-type DNA-binding domain signature. / Zn(2)-C6 fungal-type DNA-binding domain profile. / SCF-beta-TrCP mediated degradation of Emi1 / SCF(Skp2)-mediated degradation of p27/p21 / Transcriptional activator of glycolytic enzymes / Orc1 removal from chromatin / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / Neddylation / Iron uptake and transport / RAVE complex / CBF3 complex / centromeric DNA binding / mitotic spindle elongation / septin ring assembly / 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 / exit from mitosis / SCF ubiquitin ligase complex / spindle pole body / DNA binding, bending / DNA replication origin binding / condensed nuclear chromosome, centromeric region / cellular protein-containing complex assembly / 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 S288C (yeast)
Methodsingle particle reconstruction / cryo EM / 3.6 Å resolution
AuthorsYan K / Zhang Z / Yang J / McLaughlin SH / Barford D
CitationJournal: Nat. Struct. Mol. Biol. / Year: 2018
Title: Architecture of the CBF3-centromere complex of the budding yeast kinetochore.
Authors: Kaige Yan / Ziguo Zhang / Jing Yang / Stephen H McLaughlin / David Barford
Validation ReportPDB-ID: 6gyp

SummaryFull reportAbout validation report
DateDeposition: Jul 1, 2018 / Header (metadata) release: Aug 1, 2018 / Map release: Dec 5, 2018 / Last update: Dec 5, 2018

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.05
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.05
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-6gyp
  • Surface level: 0.05
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_0095.map.gz (map file in CCP4 format, 256001 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
400 pix
1.06 Å/pix.
= 424. Å
400 pix
1.06 Å/pix.
= 424. Å
400 pix
1.06 Å/pix.
= 424. 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:0.05 (by author), 0.05 (movie #1):
Minimum - Maximum-0.41150066 - 0.61012393
Average (Standard dev.)0.00017868022 (0.0071817855)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions400400400
Origin0.00.00.0
Limit399.0399.0399.0
Spacing400400400
CellA=B=C: 423.99997 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/z400400400
origin x/y/z0.0000.0000.000
length x/y/z424.000424.000424.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ450450450
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS400400400
D min/max/mean-0.4120.6100.000

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Supplemental data

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Sample components

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Entire CBF3-core-Ndc10-DBD complex

EntireName: CBF3-core-Ndc10-DBD complex / Number of components: 12

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Component #1: protein, CBF3-core-Ndc10-DBD complex

ProteinName: CBF3-core-Ndc10-DBD complex / Recombinant expression: No
SourceSpecies: Saccharomyces cerevisiae S288C (yeast)
Source (engineered)Expression System: unidentified baculovirus

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

ProteinName: Centromere DNA-binding protein complex CBF3 subunit B / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 71.439891 kDa
SourceSpecies: Saccharomyces cerevisiae S288C (yeast)
Source (engineered)Expression System: unidentified baculovirus

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Component #3: protein, Centromere DNA-binding protein complex CBF3 subunit C

ProteinName: Centromere DNA-binding protein complex CBF3 subunit C / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 56.416863 kDa
SourceSpecies: Saccharomyces cerevisiae S288C (yeast)
Source (engineered)Expression System: unidentified baculovirus

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

ProteinName: Centromere DNA-binding protein complex CBF3 subunit B / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 66.401859 kDa
SourceSpecies: Saccharomyces cerevisiae S288C (yeast)
Source (engineered)Expression System: unidentified baculovirus

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Component #5: 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 S288C (yeast)
Source (engineered)Expression System: unidentified baculovirus

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Component #6: protein, Centromere DNA-binding protein complex CBF3 subunit A

ProteinName: Centromere DNA-binding protein complex CBF3 subunit A / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 112.066031 kDa
SourceSpecies: Saccharomyces cerevisiae S288C (yeast)
Source (engineered)Expression System: unidentified baculovirus

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Component #7: ligand, METHIONINE

LigandName: METHIONINE / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 0.149211 kDa

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Component #8: ligand, PHENYLALANINE

LigandName: PHENYLALANINE / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 0.165189 kDa

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Component #9: ligand, ASPARAGINE

LigandName: ASPARAGINE / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 0.132118 kDa

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Component #10: ligand, ARGININE

LigandName: ARGININE / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 0.175209 kDa

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Component #11: ligand, THREONINE

LigandName: THREONINE / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 0.119119 kDa

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Component #12: ligand, GLUTAMINE

LigandName: GLUTAMINE / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 0.146144 kDa

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionSpecimen conc.: 0.4 mg/ml / pH: 8
VitrificationCryogen name: ETHANE

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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: 27 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: FEI FALCON III (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 73894
3D reconstructionResolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Output model

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