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- EMDB-20272: Structure of the K. lactis CBF3 core - Ndc10 D1D2 complex -

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Basic information

Entry
Database: EMDB / ID: EMD-20272
TitleStructure of the K. lactis CBF3 core - Ndc10 D1D2 complex
Map data
SampleK. lactis CBF3 core - Ndc10 D1D2 Complex:
Ndc10 / Ctf13 / Skp1 / Cep3Barrhead Airport
Function / homology
Function and homology information


ubiquitin-dependent protein catabolic process / DNA-binding transcription factor activity, RNA polymerase II-specific / zinc ion binding / integral component of membrane / nucleus
SKP1-like, dimerisation domain superfamily / Transcription activator GCR1-like domain / Skp1 family, dimerisation domain / Fungal Zn(2)-Cys(6) binuclear cluster domain / Ndc10, domain 2 superfamily / Zn(2)-C6 fungal-type DNA-binding domain superfamily / Centromere DNA-binding protein complex CBF3 subunit, domain 2 / Ndc10, domain 2 / Centromere DNA-binding protein complex CBF3 subunit B, C-terminal / S-phase kinase-associated protein 1 ...SKP1-like, dimerisation domain superfamily / Transcription activator GCR1-like domain / Skp1 family, dimerisation domain / Fungal Zn(2)-Cys(6) binuclear cluster domain / Ndc10, domain 2 superfamily / Zn(2)-C6 fungal-type DNA-binding domain superfamily / Centromere DNA-binding protein complex CBF3 subunit, domain 2 / Ndc10, domain 2 / Centromere DNA-binding protein complex CBF3 subunit B, C-terminal / S-phase kinase-associated protein 1 / Transcriptional activator of glycolytic enzymes / SKP1 component, POZ domain / SKP1 component, dimerisation / SKP1/BTB/POZ domain superfamily / S-phase kinase-associated protein 1-like / Zn(2)-C6 fungal-type DNA-binding domain / Centromere DNA-binding protein complex CBF3 subunit B / Zn(2)-C6 fungal-type DNA-binding domain profile. / Skp1 family, tetramerisation domain
Centromere-associated factor / KLLA0F13816p / KLLA0E03807p / KLLA0D09977p
Biological speciesKluyveromyces lactis (yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.3 Å
AuthorsLee PD / Wei H / Tan D / Harrison SC
Funding support United States, 2 items
OrganizationGrant numberCountry
Howard Hughes Medical Institute United States
National Institutes of Health/National Institute of General Medical Sciences
CitationJournal: J. Mol. Biol. / Year: 2019
Title: Structure of the Centromere Binding Factor 3 Complex from Kluyveromyces lactis.
Authors: Phong D Lee / Hui Wei / Dongyan Tan / Stephen C Harrison /
Abstract: Kinetochores are the multiprotein complexes that link chromosomal centromeres to mitotic-spindle microtubules. Budding yeast centromeres comprise three sequential "centromere-determining elements", ...Kinetochores are the multiprotein complexes that link chromosomal centromeres to mitotic-spindle microtubules. Budding yeast centromeres comprise three sequential "centromere-determining elements", CDEI, II, and III. CDEI (8 bp) and CDEIII (~25 bp) are conserved between Kluyveromyces lactis and Saccharomyces cerevisiae, but CDEII in the former is twice as long (160 bp) as CDEII in the latter (80 bp). The CBF3 complex recognizes CDEIII and is required for assembly of a centromeric nucleosome, which in turn recruits other kinetochore components. To understand differences in centromeric nucleosome assembly between K. lactis and S. cerevisiae, we determined the structure of a K. lactis CBF3 complex by electron cryomicroscopy at ~4 Å resolution and compared it with published structures of S. cerevisiae CBF3. We show differences in the pose of Ndc10 and discuss potential models of the K. lactis centromeric nucleosome that account for the extended CDEII length.
Validation ReportPDB-ID: 6p7x

SummaryFull reportAbout validation report
History
DepositionJun 6, 2019-
Header (metadata) releaseJul 17, 2019-
Map releaseSep 18, 2019-
UpdateSep 18, 2019-
Current statusSep 18, 2019Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.006
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.006
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-6p7x
  • Surface level: 0.006
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_20272.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 288 pix.
= 305.424 Å
1.06 Å/pix.
x 288 pix.
= 305.424 Å
1.06 Å/pix.
x 288 pix.
= 305.424 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.0605 Å
Density
Contour LevelBy AUTHOR: 0.006 / Movie #1: 0.006
Minimum - Maximum-0.012978877 - 0.03881542
Average (Standard dev.)0.00014452149 (±0.0012725573)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions288288288
Spacing288288288
CellA=B=C: 305.424 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.06051.06051.0605
M x/y/z288288288
origin x/y/z0.0000.0000.000
length x/y/z305.424305.424305.424
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS288288288
D min/max/mean-0.0130.0390.000

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Supplemental data

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Sample components

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Entire K. lactis CBF3 core - Ndc10 D1D2 Complex

EntireName: K. lactis CBF3 core - Ndc10 D1D2 Complex / Number of components: 5

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Component #1: protein, K. lactis CBF3 core - Ndc10 D1D2 Complex

ProteinName: K. lactis CBF3 core - Ndc10 D1D2 Complex / Recombinant expression: No
SourceSpecies: Kluyveromyces lactis (yeast)
Source (engineered)Expression System: Trichoplusia ni (cabbage looper)

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Component #2: protein, Ndc10

ProteinName: Ndc10 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 47.053719 kDa
SourceSpecies: Kluyveromyces lactis (yeast)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #3: protein, Ctf13

ProteinName: Ctf13 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 46.159945 kDa
SourceSpecies: Kluyveromyces lactis (yeast)
Source (engineered)Expression System: Trichoplusia ni (cabbage looper)

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Component #4: protein, Skp1

ProteinName: Skp1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 21.081141 kDa
SourceSpecies: Kluyveromyces lactis (yeast)
Source (engineered)Expression System: Trichoplusia ni (cabbage looper)

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Component #5: protein, Cep3

ProteinName: Cep3Barrhead Airport / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 74.165312 kDa
SourceSpecies: Kluyveromyces lactis (yeast)
Source (engineered)Expression System: Trichoplusia ni (cabbage looper)

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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionpH: 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: 65 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 63177
3D reconstructionResolution: 4.3 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot (resolution estimation)

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Atomic model buiding

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