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- EMDB-18745: Human Cenp-A nucleosome assembled on alpha-satellite DNA (most un... -

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Basic information

Entry
Database: EMDB / ID: EMD-18745
TitleHuman Cenp-A nucleosome assembled on alpha-satellite DNA (most unwrapped DNA)
Map dataHuman Cenp-A nucleosome assembled on alpha-satellite DNA (most unwrapped DNA)
Sample
  • Complex: Human Cenp-A nucleosome assembled on alpha-satellite DNA (most unwrapped DNA)
    • Protein or peptide: Human histone CENP-A
    • Protein or peptide: Human histone H4
    • Protein or peptide: Human histone H2A
    • Protein or peptide: Human histone H2B
    • DNA: human alpha-satellite DNA
KeywordsNucleosome / Centromere / centromeric / H3-like / CENP-A / Histones / Human / DNA / DNA BINDING PROTEIN
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.4 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 25, 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_18745.png

Downloads & links

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Map

FileDownload / File: emd_18745.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationHuman Cenp-A nucleosome assembled on alpha-satellite DNA (most unwrapped DNA)
Projections & slices

Image control

Size
Brightness
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AxesZ (Sec.)Y (Row.)X (Col.)
1.2 Å/pix.
x 256 pix.
= 308.378 Å		1.2 Å/pix.
x 256 pix.
= 308.378 Å		1.2 Å/pix.
x 256 pix.
= 308.378 Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.2046 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.102
Minimum - Maximum-0.22038946 - 0.4521906
Average (Standard dev.)-0.00054631475 (±0.016366012)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 308.3776 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_18745_msk_1.map
Projections & Slices
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Half map: #2

Fileemd_18745_half_map_1.map
Projections & Slices
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Histogram

Histogram (log scale)

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Half map: #1

Fileemd_18745_half_map_2.map
Projections & Slices
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Histogram (log scale)

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Sample components

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Entire : Human Cenp-A nucleosome assembled on alpha-satellite DNA (most un...

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

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Supramolecule #1: Human Cenp-A nucleosome assembled on alpha-satellite DNA (most un...

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

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Macromolecule #1: Human histone CENP-A

MacromoleculeName: Human histone CENP-A / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MARTKQTARK STGGKAPRKQ LATKAARKSA PATGGVKKPH RYRPGTVALR EIRKLQKSTH LLIRKLPFSR LAREICVKFT RGVDFNWQAQ ALLALQEAAE AFLVHLFEDA YLLTLHAGRV TLFPKDVQLA RRIRGLEEGL G

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Macromolecule #2: Human histone H4

MacromoleculeName: Human histone H4 / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MSGRGKGGKG LGKGGAKRHR KVLRDNIQGI TKPAIRRLAR RGGVKRISGL IYEETRGVLK VFLENVIRDA VTYTEHAKRK TVTAMDVVYA LKRQGRTLYG FGG

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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 mg/mL
BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 57.5 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: 2.2 µm / Nominal defocus min: 0.6 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 926948
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 87222
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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