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- EMDB-18699: Human H3 nucleosome assembled on alpha-satellite DNA (Class1: mos... -

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Basic information

Entry
Database: EMDB / ID: EMD-18699
TitleHuman H3 nucleosome assembled on alpha-satellite DNA (Class1: most wrapped DNA)
Map dataHuman H3 nucleosome assembled on aplha-satellite DNA
Sample
  • Complex: Human H3 nucleosome assembled on alpha-satellite DNA
    • Protein or peptide: H3 histone
    • Protein or peptide: H4 histone
    • Protein or peptide: H2A histone
    • Protein or peptide: H2B histone
    • DNA: alpha-satellite DNA
KeywordsNucleosome / canonical / H3 / Histones / Human / DNA / DNA BINDING PROTEIN
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.73 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 20, 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_18699.png

Downloads & links

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Map

FileDownload / File: emd_18699.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationHuman H3 nucleosome assembled on aplha-satellite DNA
Projections & slices

Image control

Size
Brightness
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.7 Å/pix.
x 360 pix.
= 253.44 Å		0.7 Å/pix.
x 360 pix.
= 253.44 Å		0.7 Å/pix.
x 360 pix.
= 253.44 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.704 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.042
Minimum - Maximum-0.13889581 - 0.29203454
Average (Standard dev.)-0.000044384145 (±0.009307511)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 253.44 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_18699_msk_1.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Half map: #2

Fileemd_18699_half_map_1.map
Projections & Slices
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Histogram

Histogram (log scale)

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Half map: #1

Fileemd_18699_half_map_2.map
Projections & Slices
AxesZYX

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Histogram (log scale)

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Sample components

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Entire : Human H3 nucleosome assembled on alpha-satellite DNA

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

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Supramolecule #1: Human H3 nucleosome assembled on alpha-satellite DNA

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

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Macromolecule #1: H3 histone

MacromoleculeName: H3 histone / 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: H4 histone

MacromoleculeName: 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: H2A histone

MacromoleculeName: H2A histone / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
SGMKETAAAK FERQHMDSPD LGTLEVLFQG PLGMSGRGKQ GGKARAKAKS RSSRAGLQFP VGRVHRLLRK GNYAERVGAG APVYMAAVLE YLTAEILELA GNAARDNKKT RIIPRHLQLA IRNDEELNKL LGKVTIAQGG VLPNIQAVLL PKKTESHHKA KGK

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Macromolecule #4: H2B histone

MacromoleculeName: H2B histone / 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: alpha-satellite DNA

MacromoleculeName: 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
GridMaterial: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 45 sec.
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: 2.73 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 242755
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final 3D classificationNumber classes: 2
FSC plot (resolution estimation)

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