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- EMDB-4579: Structure of inner kinetochore CCAN-Cenp-A complex -

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Entry
Database: EMDB / ID: EMD-4579
TitleStructure of inner kinetochore CCAN-Cenp-A complex
Map data
SampleInner kinetochore CCAN complex assembled onto a centromeric nucleosome
  • kinetochore
  • DNA
  • HistonesHistone
  • (Inner kinetochore subunit ...) x 12
  • (nucleic-acidNucleic acid) x 2
  • (Histone H3-like centromeric protein ...) x 2
  • Histone H4
  • Histone H2B.2
  • (Histone H2A.1) x 2
  • Histone H2B.1
Function / homology
Function and homology information


HATs acetylate histones / Estrogen-dependent gene expression / SUMOylation of chromatin organization proteins / RMTs methylate histone arginines / HDMs demethylate histones / Oxidative Stress Induced Senescence / Condensation of Prophase Chromosomes / protein localization to CENP-A containing chromatin / negative regulation of meiotic DNA double-strand break formation involved in reciprocal meiotic recombination / Mis6-Sim4 complex ...HATs acetylate histones / Estrogen-dependent gene expression / SUMOylation of chromatin organization proteins / RMTs methylate histone arginines / HDMs demethylate histones / Oxidative Stress Induced Senescence / Condensation of Prophase Chromosomes / protein localization to CENP-A containing chromatin / negative regulation of meiotic DNA double-strand break formation involved in reciprocal meiotic recombination / Mis6-Sim4 complex / COMA complex / 2-micrometer circle DNA / establishment of meiotic sister chromatid cohesion / maintenance of meiotic sister chromatid cohesion / 2-micrometer plasmid partitioning / centromere complex assembly / meiotic sister chromatid segregation / CENP-A containing nucleosome / transfer RNA gene-mediated silencing / attachment of spindle microtubules to kinetochore involved in homologous chromosome segregation / attachment of spindle microtubules to kinetochore / sexual sporulation resulting in formation of a cellular spore / ascospore formation / centromeric DNA binding / establishment of mitotic sister chromatid cohesion / attachment of mitotic spindle microtubules to kinetochore / histone H3-K79 methylation / condensed nuclear chromosome outer kinetochore / protein localization to chromosome, centromeric region / kinetochore assembly / chromatin assembly or disassembly / replication fork protection complex / condensed nuclear chromosome kinetochore / spindle pole body / postreplication repair / protein localization to kinetochore / condensed nuclear chromosome, centromeric region / DNA replication initiation / rRNA transcription / condensed chromosome kinetochore / mitotic spindle assembly checkpoint / mitotic sister chromatid segregation / nuclear nucleosome / nucleosomal DNA binding / mitotic spindle organization / kinetochore / chromosome segregation / meiotic cell cycle / nucleosome assembly / nucleosome / chromatin organization / sequence-specific DNA binding / protein-containing complex binding / cell division / nuclear chromatin / DNA repair / structural molecule activity / protein heterodimerization activity / negative regulation of transcription by RNA polymerase II / DNA binding / nucleus / cytoplasm
Histone H2A, C-terminal domain / Histone H2B / Histone H2A/H2B/H3 / Histone H2A signature. / C-terminus of histone H2A / Kinetochore CENP-C fungal homologue, Mif2, N-terminal / Histone H2A / Histone H4 / Histone H3/CENP-A / Centromere protein Chl4/mis15/CENP-N ...Histone H2A, C-terminal domain / Histone H2B / Histone H2A/H2B/H3 / Histone H2A signature. / C-terminus of histone H2A / Kinetochore CENP-C fungal homologue, Mif2, N-terminal / Histone H2A / Histone H4 / Histone H3/CENP-A / Centromere protein Chl4/mis15/CENP-N / CENP-T/Histone H4, histone fold / Core histone H2A/H2B/H3/H4 / Centromere kinetochore component CENP-T histone fold / Kinetochore protein CHL4 like / Cnl2/NKP2 family protein / Histone H2A conserved site / Histone H4 signature. / Histone H2B signature. / Mif2/CENP-C like / Mif2/cnp3, N-terminal / Centromere protein C/Mif2/cnp3 / Mif2/CENP-C cupin domain / Histone H4, conserved site / Histone-fold / Kinetochore subunit Nkp2/Cnl2 / Centromere protein O / Histone H3 signature 2. / RmlC-like jelly roll fold / Cenp-O kinetochore centromere component
Inner kinetochore subunit NKP1 / Inner kinetochore subunit MCM16 / Inner kinetochore subunit MCM21 / Inner kinetochore subunit NKP2 / Inner kinetochore subunit CTF19 / Inner kinetochore subunit OKP1 / Inner kinetochore subunit MCM22 / Inner kinetochore subunit AME1 / Inner kinetochore subunit CHL4 / Inner kinetochore subunit IML3 ...Inner kinetochore subunit NKP1 / Inner kinetochore subunit MCM16 / Inner kinetochore subunit MCM21 / Inner kinetochore subunit NKP2 / Inner kinetochore subunit CTF19 / Inner kinetochore subunit OKP1 / Inner kinetochore subunit MCM22 / Inner kinetochore subunit AME1 / Inner kinetochore subunit CHL4 / Inner kinetochore subunit IML3 / Histone H3-like centromeric protein CSE4 / Inner kinetochore subunit MIF2 / Histone H2A.1 / Histone H4 / Histone H2B.2 / Histone H2B.1 / Inner kinetochore subunit CTF3
Biological speciesSaccharomyces cerevisiae (strain ATCC 204508 / S288c) cerevisiae (yeast) / Escherichia coli (E. coli) / Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.15 Å
AuthorsYan K / Yang J / Zhang Z / McLaughlin SH / Chang L / Fasci D / Heck AJR / Barford D
Funding support United Kingdom, 3 items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)MC_UP_1201/6 United Kingdom
European CommissionINFRAIA project Epic-XS (Project 823839)
Cancer Research UKC576/A14109 United Kingdom
CitationJournal: Nature / Year: 2019
Title: Structure of the inner kinetochore CCAN complex assembled onto a centromeric nucleosome.
Authors: Kaige Yan / Jing Yang / Ziguo Zhang / Stephen H McLaughlin / Leifu Chang / Domenico Fasci / Ann E Ehrenhofer-Murray / Albert J R Heck / David Barford /
Abstract: In eukaryotes, accurate chromosome segregation in mitosis and meiosis maintains genome stability and prevents aneuploidy. Kinetochores are large protein complexes that, by assembling onto specialized ...In eukaryotes, accurate chromosome segregation in mitosis and meiosis maintains genome stability and prevents aneuploidy. Kinetochores are large protein complexes that, by assembling onto specialized Cenp-A nucleosomes, function to connect centromeric chromatin to microtubules of the mitotic spindle. Whereas the centromeres of vertebrate chromosomes comprise millions of DNA base pairs and attach to multiple microtubules, the simple point centromeres of budding yeast are connected to individual microtubules. All 16 budding yeast chromosomes assemble complete kinetochores using a single Cenp-A nucleosome (Cenp-A), each of which is perfectly centred on its cognate centromere. The inner and outer kinetochore modules are responsible for interacting with centromeric chromatin and microtubules, respectively. Here we describe the cryo-electron microscopy structure of the Saccharomyces cerevisiae inner kinetochore module, the constitutive centromere associated network (CCAN) complex, assembled onto a Cenp-A nucleosome (CCAN-Cenp-A). The structure explains the interdependency of the constituent subcomplexes of CCAN and shows how the Y-shaped opening of CCAN accommodates Cenp-A to enable specific CCAN subunits to contact the nucleosomal DNA and histone subunits. Interactions with the unwrapped DNA duplex at the two termini of Cenp-A are mediated predominantly by a DNA-binding groove in the Cenp-L-Cenp-N subcomplex. Disruption of these interactions impairs assembly of CCAN onto Cenp-A. Our data indicate a mechanism of Cenp-A nucleosome recognition by CCAN and how CCAN acts as a platform for assembly of the outer kinetochore to link centromeres to the mitotic spindle for chromosome segregation.
Validation ReportPDB-ID: 6qld

SummaryFull reportAbout validation report
History
DepositionJan 31, 2019-
Header (metadata) releaseJul 31, 2019-
Map releaseOct 2, 2019-
UpdateOct 2, 2019-
Current statusOct 2, 2019Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.017
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.017
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-6qld
  • Surface level: 0.017
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_4579.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.09 Å/pix.
x 320 pix.
= 348.8 Å
1.09 Å/pix.
x 320 pix.
= 348.8 Å
1.09 Å/pix.
x 320 pix.
= 348.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.09 Å
Density
Contour LevelBy AUTHOR: 0.017 / Movie #1: 0.017
Minimum - Maximum-0.06863052 - 0.12158532
Average (Standard dev.)0.00029283442 (±0.0026867972)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 348.80002 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.091.091.09
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z348.800348.800348.800
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ320320320
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS320320320
D min/max/mean-0.0690.1220.000

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Supplemental data

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Sample components

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Entire Inner kinetochore CCAN complex assembled onto a centromeric nucleosome

EntireName: Inner kinetochore CCAN complex assembled onto a centromeric nucleosome
Number of components: 25

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Component #1: protein, Inner kinetochore CCAN complex assembled onto a centrome...

ProteinName: Inner kinetochore CCAN complex assembled onto a centromeric nucleosome
Recombinant expression: No

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Component #2: protein, kinetochore

ProteinName: kinetochore / Recombinant expression: No
SourceSpecies: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) cerevisiae (yeast)
Source (engineered)Expression System: Trichoplusia ni (cabbage looper)

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Component #3: protein, DNA

ProteinName: DNA / Recombinant expression: No
SourceSpecies: Escherichia coli (E. coli)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #4: protein, Histones

ProteinName: HistonesHistone / Recombinant expression: No
SourceSpecies: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #5: protein, Inner kinetochore subunit MIF2

ProteinName: Inner kinetochore subunit MIF2 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 2.754279 kDa
SourceSpecies: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Source (engineered)Expression System: Trichoplusia ni (cabbage looper)

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Component #6: nucleic-acid, DNA (125-MER)

nucleic acidName: DNA (125-MER) / Class: DNA / Structure: OTHER / Synthetic: No
Sequence:
(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) (DC)(DC)(DG)(DC)(DC)(DA)(DA)(DG)(DG)(DG) (DG)(DA)(DT)(DT)(DA)(DC)(DT)(DC)(DC)(DC) (DT)(DA)(DG)(DT)(DC)(DT)(DC)(DC)(DA)(DG) (DG)(DC)(DA)(DC)
MassTheoretical: 38.030211 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #7: protein, Inner kinetochore subunit MCM16

ProteinName: Inner kinetochore subunit MCM16 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 15.815147 kDa
SourceSpecies: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Source (engineered)Expression System: Trichoplusia ni (cabbage looper)

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Component #8: protein, Inner kinetochore subunit CTF3

ProteinName: Inner kinetochore subunit CTF3 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 47.222789 kDa
SourceSpecies: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Source (engineered)Expression System: Trichoplusia ni (cabbage looper)

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Component #9: nucleic-acid, DNA (125-MER)

nucleic acidName: DNA (125-MER) / Class: DNA / Structure: OTHER / Synthetic: No
Sequence:
(DG)(DT)(DG)(DC)(DC)(DT)(DG)(DG)(DA)(DG) (DA)(DC)(DT)(DA)(DG)(DG)(DG)(DA)(DG)(DT) (DA)(DA)(DT)(DC)(DC)(DC)(DC)(DT)(DT)(DG) (DG)(DC)(DG)(DG)(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)
MassTheoretical: 38.510504 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #10: protein, Inner kinetochore subunit MCM22

ProteinName: Inner kinetochore subunit MCM22 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 14.082116 kDa
SourceSpecies: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Source (engineered)Expression System: Trichoplusia ni (cabbage looper)

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Component #11: protein, Inner kinetochore subunit IML3

ProteinName: Inner kinetochore subunit IML3 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 27.64473 kDa
SourceSpecies: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Source (engineered)Expression System: Trichoplusia ni (cabbage looper)

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Component #12: protein, Inner kinetochore subunit CHL4

ProteinName: Inner kinetochore subunit CHL4 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 51.64243 kDa
SourceSpecies: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Source (engineered)Expression System: Trichoplusia ni (cabbage looper)

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Component #13: protein, Inner kinetochore subunit MCM21

ProteinName: Inner kinetochore subunit MCM21 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 24.746383 kDa
SourceSpecies: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Source (engineered)Expression System: Trichoplusia ni (cabbage looper)

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Component #14: protein, Inner kinetochore subunit CTF19

ProteinName: Inner kinetochore subunit CTF19 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 31.659006 kDa
SourceSpecies: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Source (engineered)Expression System: Trichoplusia ni (cabbage looper)

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Component #15: protein, Inner kinetochore subunit OKP1

ProteinName: Inner kinetochore subunit OKP1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 27.358393 kDa
SourceSpecies: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Source (engineered)Expression System: Trichoplusia ni (cabbage looper)

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Component #16: protein, Inner kinetochore subunit AME1

ProteinName: Inner kinetochore subunit AME1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 22.157994 kDa
SourceSpecies: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Source (engineered)Expression System: Trichoplusia ni (cabbage looper)

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Component #17: protein, Inner kinetochore subunit NKP1

ProteinName: Inner kinetochore subunit NKP1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 26.875254 kDa
SourceSpecies: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Source (engineered)Expression System: Trichoplusia ni (cabbage looper)

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Component #18: protein, Inner kinetochore subunit NKP2

ProteinName: Inner kinetochore subunit NKP2 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 17.631734 kDa
SourceSpecies: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Source (engineered)Expression System: Trichoplusia ni (cabbage looper)

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Component #19: protein, Histone H3-like centromeric protein CSE4

ProteinName: Histone H3-like centromeric protein CSE4 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 10.535404 kDa
SourceSpecies: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #20: protein, Histone H4

ProteinName: Histone H4 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 8.897329 kDa
SourceSpecies: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #21: protein, Histone H2B.2

ProteinName: Histone H2B.2 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 10.342754 kDa
SourceSpecies: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #22: protein, Histone H3-like centromeric protein CSE4

ProteinName: Histone H3-like centromeric protein CSE4 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 13.715144 kDa
SourceSpecies: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #23: protein, Histone H2A.1

ProteinName: Histone H2A.1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 11.546386 kDa
SourceSpecies: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #24: protein, Histone H2B.1

ProteinName: Histone H2B.1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 10.413832 kDa
SourceSpecies: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #25: protein, Histone H2A.1

ProteinName: Histone H2A.1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 11.190911 kDa
SourceSpecies: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Source (engineered)Expression System: Escherichia coli (E. coli)

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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionSpecimen conc.: 1 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: 32 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: 145783
3D reconstructionResolution: 4.15 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Output model

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