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- EMDB-22698: nucleosome and Gal4 complex -

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Basic information

Entry
Database: EMDB / ID: EMD-22698
Titlenucleosome and Gal4 complex
Map data
Samplethe nucleosome and Gal4 domain complex
  • Histone H3
  • Histone H4
  • Histone H2A.1
  • Histone H2B.1
  • (nucleic-acidNucleic acid) x 2
  • Centromere DNA-binding protein complex CBF3 subunit B
  • ligand
Function / homology
Function and homology information


CBF3 complex / CENP-A containing nucleosome / septin ring assembly / sexual sporulation resulting in formation of a cellular spore / transfer RNA gene-mediated silencing / centromeric DNA binding / histone H3-K79 methylation / replication fork protection complex / chromatin assembly or disassembly / kinetochore => GO:0000776 ...CBF3 complex / CENP-A containing nucleosome / septin ring assembly / sexual sporulation resulting in formation of a cellular spore / transfer RNA gene-mediated silencing / centromeric DNA binding / histone H3-K79 methylation / replication fork protection complex / chromatin assembly or disassembly / kinetochore => GO:0000776 / postreplication repair / DNA binding, bending / mitotic spindle assembly checkpoint signaling / rRNA transcription / chromatin silencing / global genome nucleotide-excision repair / nucleosome assembly / nucleosome / DNA-binding transcription factor activity, RNA polymerase II-specific / protein heterodimerization activity / DNA repair / negative regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / identical protein binding / nucleus
Histone H4, conserved site / Centromere DNA-binding protein complex CBF3 subunit B, C-terminal / Histone-fold / Histone H2A/H2B/H3 / Zn(2)-C6 fungal-type DNA-binding domain superfamily / CENP-T/Histone H4, histone fold / Histone H2A / Histone H4 / Zn(2)-C6 fungal-type DNA-binding domain / Histone H2B ...Histone H4, conserved site / Centromere DNA-binding protein complex CBF3 subunit B, C-terminal / Histone-fold / Histone H2A/H2B/H3 / Zn(2)-C6 fungal-type DNA-binding domain superfamily / CENP-T/Histone H4, histone fold / Histone H2A / Histone H4 / Zn(2)-C6 fungal-type DNA-binding domain / Histone H2B / Histone H3/CENP-A / Histone H2A conserved site / Histone H2A, C-terminal domain
Histone H2B.1 / Histone H4 / Histone H2A.1 / Centromere DNA-binding protein complex CBF3 subunit B / Histone H3
Biological speciesSaccharomyces cerevisiae (baker's yeast) / Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.2 Å
AuthorsRuifang G / Yawen B
CitationJournal: Nat Commun / Year: 2021
Title: Structural and dynamic mechanisms of CBF3-guided centromeric nucleosome formation.
Authors: Ruifang Guan / Tengfei Lian / Bing-Rui Zhou / Emily He / Carl Wu / Martin Singleton / Yawen Bai /
Abstract: Accurate chromosome segregation relies on the specific centromeric nucleosome-kinetochore interface. In budding yeast, the centromere CBF3 complex guides the deposition of CENP-A, an H3 variant, to ...Accurate chromosome segregation relies on the specific centromeric nucleosome-kinetochore interface. In budding yeast, the centromere CBF3 complex guides the deposition of CENP-A, an H3 variant, to form the centromeric nucleosome in a DNA sequence-dependent manner. Here, we determine the structures of the centromeric nucleosome containing the native CEN3 DNA and the CBF3core bound to the canonical nucleosome containing an engineered CEN3 DNA. The centromeric nucleosome core structure contains 115 base pair DNA including a CCG motif. The CBF3core specifically recognizes the nucleosomal CCG motif through the Gal4 domain while allosterically altering the DNA conformation. Cryo-EM, modeling, and mutational studies reveal that the CBF3core forms dynamic interactions with core histones H2B and CENP-A in the CEN3 nucleosome. Our results provide insights into the structure of the budding yeast centromeric nucleosome and the mechanism of its assembly, which have implications for analogous processes of human centromeric nucleosome formation.
Validation ReportSummary, Full report, XML, About validation report
History
DepositionSep 22, 2020-
Header (metadata) releaseMar 31, 2021-
Map releaseMar 31, 2021-
UpdateMar 31, 2021-
Current statusMar 31, 2021Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.02
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.02
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7k7g
  • Surface level: 0.02
  • 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_22698.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 280 pix.
= 296.8 Å
1.06 Å/pix.
x 280 pix.
= 296.8 Å
1.06 Å/pix.
x 280 pix.
= 296.8 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 LevelBy AUTHOR: 0.02 / Movie #1: 0.02
Minimum - Maximum-0.017226133 - 0.062269825
Average (Standard dev.)0.0001518656 (±0.0022766711)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 296.8 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.061.061.06
M x/y/z280280280
origin x/y/z0.0000.0000.000
length x/y/z296.800296.800296.800
α/β/γ90.00090.00090.000
start NX/NY/NZ15150
NX/NY/NZ9999114
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS280280280
D min/max/mean-0.0170.0620.000

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Supplemental data

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Sample components

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Entire the nucleosome and Gal4 domain complex

EntireName: the nucleosome and Gal4 domain complex / Number of components: 9

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Component #1: protein, the nucleosome and Gal4 domain complex

ProteinName: the nucleosome and Gal4 domain complex / Recombinant expression: No
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)
Source (engineered)Expression System: Escherichia phage EcSzw-2 (bacteriophage)

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Component #2: protein, Histone H3

ProteinName: Histone H3 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 15.391007 kDa
SourceSpecies: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Source (engineered)Expression System: Escherichia phage EcSzw-2 (bacteriophage)

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Component #3: protein, Histone H4

ProteinName: Histone H4 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 11.39539 kDa
SourceSpecies: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Source (engineered)Expression System: Escherichia phage EcSzw-2 (bacteriophage)

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Component #4: protein, Histone H2A.1

ProteinName: Histone H2A.1 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 14.013177 kDa
SourceSpecies: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Source (engineered)Expression System: Escherichia phage EcSzw-2 (bacteriophage)

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Component #5: protein, Histone H2B.1

ProteinName: Histone H2B.1 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 14.280362 kDa
SourceSpecies: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Source (engineered)Expression System: Escherichia phage EcSzw-2 (bacteriophage)

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Component #6: nucleic-acid, DNA (147-MER)

nucleic acidName: DNA (147-MER) / Class: DNA / Structure: OTHER / Synthetic: No
Sequence: (DA)(DT)(DC)(DG)(DA)(DG)(DA)(DA)(DT)(DC) (DC)(DC)(DG)(DG)(DT)(DG)(DC)(DC)(DG)(DA) (DG)(DG)(DC)(DC)(DG)(DC)(DT)(DC)(DA)(DA) (DT)(DT)(DG)(DG)(DT)(DC)(DG)(DT)(DA)(DG) (DA)(DC)(DA)(DG)(DC)(DT) ...Sequence:
(DA)(DT)(DC)(DG)(DA)(DG)(DA)(DA)(DT)(DC) (DC)(DC)(DG)(DG)(DT)(DG)(DC)(DC)(DG)(DA) (DG)(DG)(DC)(DC)(DG)(DC)(DT)(DC)(DA)(DA) (DT)(DT)(DG)(DG)(DT)(DC)(DG)(DT)(DA)(DG) (DA)(DC)(DA)(DG)(DC)(DT)(DC)(DT)(DA)(DG) (DC)(DA)(DC)(DC)(DG)(DC)(DT)(DT)(DA)(DA) (DA)(DC)(DG)(DC)(DA)(DC)(DG)(DT)(DA)(DC) (DG)(DC)(DG)(DC)(DT)(DG)(DT)(DC)(DC)(DC) (DC)(DC)(DG)(DC)(DG)(DT)(DT)(DT)(DT)(DA) (DA)(DT)(DA)(DT)(DT)(DA)(DG)(DT)(DG)(DT) (DA)(DT)(DT)(DT)(DG)(DA)(DT)(DT)(DT)(DC) (DC)(DG)(DA)(DA)(DA)(DG)(DT)(DT)(DA)(DA) (DA)(DA)(DA)(DA)(DG)(DA)(DA)(DA)(DT)(DA) (DG)(DT)(DA)(DA)(DG)(DA)(DA)(DA)(DT)(DC) (DA)(DT)(DC)(DC)(DG)(DA)(DT)
MassTheoretical: 45.334012 kDa
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)

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Component #7: nucleic-acid, DNA (147-MER)

nucleic acidName: DNA (147-MER) / Class: DNA / Structure: OTHER / Synthetic: No
Sequence: (DA)(DT)(DC)(DG)(DG)(DA)(DT)(DG)(DA)(DT) (DT)(DT)(DC)(DT)(DT)(DA)(DC)(DT)(DA)(DT) (DT)(DT)(DC)(DT)(DT)(DT)(DT)(DT)(DT)(DA) (DA)(DC)(DT)(DT)(DT)(DC)(DG)(DG)(DA)(DA) (DA)(DT)(DC)(DA)(DA)(DA) ...Sequence:
(DA)(DT)(DC)(DG)(DG)(DA)(DT)(DG)(DA)(DT) (DT)(DT)(DC)(DT)(DT)(DA)(DC)(DT)(DA)(DT) (DT)(DT)(DC)(DT)(DT)(DT)(DT)(DT)(DT)(DA) (DA)(DC)(DT)(DT)(DT)(DC)(DG)(DG)(DA)(DA) (DA)(DT)(DC)(DA)(DA)(DA)(DT)(DA)(DC)(DA) (DC)(DT)(DA)(DA)(DT)(DA)(DT)(DT)(DA)(DA) (DA)(DA)(DC)(DG)(DC)(DG)(DG)(DG)(DG)(DG) (DA)(DC)(DA)(DG)(DC)(DG)(DC)(DG)(DT)(DA) (DC)(DG)(DT)(DG)(DC)(DG)(DT)(DT)(DT)(DA) (DA)(DG)(DC)(DG)(DG)(DT)(DG)(DC)(DT)(DA) (DG)(DA)(DG)(DC)(DT)(DG)(DT)(DC)(DT)(DA) (DC)(DG)(DA)(DC)(DC)(DA)(DA)(DT)(DT)(DG) (DA)(DG)(DC)(DG)(DG)(DC)(DC)(DT)(DC)(DG) (DG)(DC)(DA)(DC)(DC)(DG)(DG)(DG)(DA)(DT) (DT)(DC)(DT)(DC)(DG)(DA)(DT)
MassTheoretical: 45.399992 kDa
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)

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Component #8: 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: 5.605748 kDa
SourceSpecies: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Source (engineered)Expression System: Saccharomyces cerevisiae (baker's yeast)

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Component #9: ligand, ZINC ION

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

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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionpH: 7.3
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: 71 e/Å2 / Illumination mode: SPOT SCAN
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 115666
3D reconstructionResolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Output model

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