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- EMDB-18714: Human H3 nucleosome assembled on alpha-satellite DNA (most unwrapped) -

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Basic information

Entry
Database: EMDB / ID: EMD-18714
TitleHuman H3 nucleosome assembled on alpha-satellite DNA (most unwrapped)
Map dataHuman H3 nucleosome assembled on alpha-satellite DNA (most unwrapped)
Sample
  • Complex: Human H3 nucleosome assembled on alpha-satellite DNA (most unwrapped)
    • Protein or peptide: Human histone H3
    • Protein or peptide: Human H4 histone
    • Protein or peptide: Human histone H2A
    • Protein or peptide: Human histone H2B
  • DNA: human alpha-satellite DNA
KeywordsNucleosome / canonical / H3 / Histones / Human / DNA / DNA BINDING PROTEIN
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsAli-Ahmad A / Sekulic N
Funding support Norway, 2 items
OrganizationGrant numberCountry
Research Council of Norway187615 Norway
Research Council of Norway325528 Norway
CitationJournal: Nat Commun / Year: 2023
Title: CENP-A and CENP-B collaborate to create an open centromeric chromatin state.
Authors: Harsh Nagpal / Ahmad Ali-Ahmad / Yasuhiro Hirano / Wei Cai / Mario Halic / Tatsuo Fukagawa / Nikolina Sekulić / Beat Fierz /
Abstract: Centromeres are epigenetically defined via the presence of the histone H3 variant CENP-A. Contacting CENP-A nucleosomes, the constitutive centromere associated network (CCAN) and the kinetochore ...Centromeres are epigenetically defined via the presence of the histone H3 variant CENP-A. Contacting CENP-A nucleosomes, the constitutive centromere associated network (CCAN) and the kinetochore assemble, connecting the centromere to spindle microtubules during cell division. The DNA-binding centromeric protein CENP-B is involved in maintaining centromere stability and, together with CENP-A, shapes the centromeric chromatin state. The nanoscale organization of centromeric chromatin is not well understood. Here, we use single-molecule fluorescence and cryoelectron microscopy (cryoEM) to show that CENP-A incorporation establishes a dynamic and open chromatin state. The increased dynamics of CENP-A chromatin create an opening for CENP-B DNA access. In turn, bound CENP-B further opens the chromatin fiber structure and induces nucleosomal DNA unwrapping. Finally, removal of CENP-A increases CENP-B mobility in cells. Together, our studies show that the two centromere-specific proteins collaborate to reshape chromatin structure, enabling the binding of centromeric factors and establishing a centromeric chromatin state.
History
DepositionOct 24, 2023-
Header (metadata) releaseDec 13, 2023-
Map releaseDec 13, 2023-
UpdateDec 27, 2023-
Current statusDec 27, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_18714.png

Downloads & links

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Map

FileDownload / File: emd_18714.map.gz / Format: CCP4 / Size: 15.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationHuman H3 nucleosome assembled on alpha-satellite DNA (most unwrapped)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.58 Å/pix.
x 160 pix.
= 253.44 Å		1.58 Å/pix.
x 160 pix.
= 253.44 Å		1.58 Å/pix.
x 160 pix.
= 253.44 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.584 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.263
Minimum - Maximum-0.64049226 - 1.428339
Average (Standard dev.)-0.00047821904 (±0.03897612)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions160160160
Spacing160160160
CellA=B=C: 253.44 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_18714_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_18714_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Human H3 nucleosome assembled on alpha-satellite DNA (most unwrapped)

EntireName: Human H3 nucleosome assembled on alpha-satellite DNA (most unwrapped)
Components
  • Complex: Human H3 nucleosome assembled on alpha-satellite DNA (most unwrapped)
    • Protein or peptide: Human histone H3
    • Protein or peptide: Human H4 histone
    • Protein or peptide: Human histone H2A
    • Protein or peptide: Human histone H2B
  • DNA: human alpha-satellite DNA

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Supramolecule #1: Human H3 nucleosome assembled on alpha-satellite DNA (most unwrapped)

SupramoleculeName: Human H3 nucleosome assembled on alpha-satellite DNA (most unwrapped)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Human histone H3

MacromoleculeName: Human histone H3 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
GSMARTKQTA RKSTGGKAPR KQLATKAARK SAPSTGGVKK PHRYRPGTVA LREIRRYQKS TELLIRKLPF QRLVREIAQD FKTDLRFQSA AIGALQEASE AYLVGLFEDT NLCAIHAKRV TIMPKDIQLA RRIRGERA

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Macromolecule #2: Human H4 histone

MacromoleculeName: Human H4 histone / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
GSMSGRGKGG KGLGKGGAKR HRKVLRDNIQ GITKPAIRRL ARRGGVKRIS GLIYEETRGV LKVFLENVIR DAVTYTEHAK RKTVTAMDVV YALKRQGRTL YGFGG

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Macromolecule #3: Human histone H2A

MacromoleculeName: Human histone H2A / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
GPLGMSGRGK QGGKARAKAK SRSSRAGLQF PVGRVHRLLR KGNYAERVGA GAPVYMAAVL EYLTAEILEL AGNAARDNKK TRIIPRHLQL AIRNDEELNK LLGKVTIAQG GVLPNIQAVL LPKKTESHHK AKGK

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Macromolecule #4: Human histone H2B

MacromoleculeName: Human histone H2B / type: protein_or_peptide / ID: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MPEPAKSAPA PKKGSKKAVT KAQKKDGKKR KRSRKESYSV YVYKVLKQVH PDTGISSKAM GIMNSFVNDI FERIAGEASR LAHYNKRSTI TSREIQTAVR LLLPGELAKH AVSEGTKAVT KYTSSK

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Macromolecule #5: human alpha-satellite DNA

MacromoleculeName: human alpha-satellite DNA / type: dna / ID: 5 / Classification: DNA
Source (natural)Organism: Homo sapiens (human)
SequenceString:
GGAGGATTTC GTTGGAAACG GGATCAACTT CCCATAACTG AACGGAAGCA AACTCAGAAC ATTCTTTGTG ATGTTTGTAT TCAACTCACA GAGTTGAACC TTCCTTTGAT AGTTCAGGTT TGCAACACCC TTGTAGTAGA ATCTGCAAGT GTATATTTTG ACCACTTTGG A

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration1.1 mg/mL
BufferpH: 7.5
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 6 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.4 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 326847
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 84092
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final 3D classificationNumber classes: 2
FSC plot (resolution estimation)

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