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- EMDB-20270: Structure of the K. lactis CBF3 core -

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Basic information

Entry
Database: EMDB / ID: EMD-20270
TitleStructure of the K. lactis CBF3 core
Map data
SampleK. lactis CBF3 core:
Ctf13 / Skp1S-phase kinase-associated protein 1 / Cep3
Function / homology
Function and homology information


ubiquitin-dependent protein catabolic process / DNA-binding transcription factor activity, RNA polymerase II-specific / host cell nucleus / zinc ion binding / integral component of membrane
SKP1 component, dimerisation / S-phase kinase-associated protein 1 / Zn(2)-C6 fungal-type DNA-binding domain superfamily / SKP1-like, dimerisation domain superfamily / Centromere DNA-binding protein complex CBF3 subunit B, C-terminal / Zn(2)-C6 fungal-type DNA-binding domain / S-phase kinase-associated protein 1-like / SKP1/BTB/POZ domain superfamily / SKP1 component, POZ domain
E3 ubiquitin ligase complex SCF subunit / KLLA0F13816p / KLLA0D09977p
Biological speciesKluyveromyces lactis (yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 4 Å
AuthorsLee PD / Wei H / Tan D / Harrison SC
Funding support United States, 2 items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: Journal of molecular biology / 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: 6p7v

SummaryFull reportAbout validation report
History
DepositionJun 6, 2019-
Header (metadata) releaseJul 17, 2019-
Map releaseSep 11, 2019-
UpdateDec 11, 2019-
Current statusDec 11, 2019Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.015
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.015
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6p7v
  • Surface level: 0.015
  • 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_20270.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: 0.015 / Movie #1: 0.015
Minimum - Maximum-0.023955204 - 0.0514911
Average (Standard dev.)0.00013362462 (±0.0013920761)
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
start NX/NY/NZ-200-200-200
NX/NY/NZ401401401
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS288288288
D min/max/mean-0.0240.0510.000

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Supplemental data

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Half map: K. lactis CBF3 core, half map 1

Fileemd_20270_half_map_1.map
AnnotationK. lactis CBF3 core, half map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Half map: K. lactis CBF3 core, half map 2

Fileemd_20270_half_map_2.map
AnnotationK. lactis CBF3 core, half map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Sample components

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Entire K. lactis CBF3 core

EntireName: K. lactis CBF3 core / Number of components: 4

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Component #1: protein, K. lactis CBF3 core

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

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Component #2: 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 #3: protein, Skp1

ProteinName: Skp1S-phase kinase-associated protein 1 / 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 #4: protein, Cep3

ProteinName: Cep3 / 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
Support filmunspecified
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: 130143
3D reconstructionResolution: 4 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot (resolution estimation)

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Atomic model buiding

Output model

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