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- EMDB-51647: H3/H4 di-tetrasome assembled on alpha-satellite DNA (open conform... -

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Basic information

Entry
Database: EMDB / ID: EMD-51647
TitleH3/H4 di-tetrasome assembled on alpha-satellite DNA (open conformation).
Map data2x(H3/H4)2 di-tetrasome assembled on alpha-satellite DNA.
Sample
  • Complex: 2x(H3/H4)2 di-tetrasome assembled on alpha-satellite DNA.
    • Protein or peptide: Human H3 histone
    • Protein or peptide: Human H3 histone
    • Protein or peptide: Human H3 histone
    • Protein or peptide: Human H3 histone
    • Protein or peptide: Human H4 histone
    • Protein or peptide: Human H4 histone
    • Protein or peptide: Human H4 histone
    • Protein or peptide: Human H4 histone
    • DNA: Human alpha-satellite DNA
    • DNA: Human alpha-satellite DNA
KeywordsH3/H4 / di-tetrasome / nucleosome / centromere / CENP-A / Human / Cell division. / DNA BINDING PROTEIN
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.75 Å
AuthorsAli-Ahmad A / Sekulic N
Funding support Norway, 2 items
OrganizationGrant numberCountry
Research Council of Norway87615 Norway
Research Council of Norway325528 Norway
CitationJournal: bioRxiv / Year: 2025
Title: Non-nucleosomal (CENP-A/H4) - DNA complexes as a possible platform for centromere organization.
Authors: Ahmad Ali-Ahmad / Mira Mors / Manuel Carrer / Xinmeng Li / Silvija Bilokapić / Mario Halić / Michele Cascella / Nikolina Sekulić /
Abstract: The centromere is a part of the chromosome that is essential for the even segregation of duplicated chromosomes during cell division. It is epigenetically defined by the presence of the histone H3 ...The centromere is a part of the chromosome that is essential for the even segregation of duplicated chromosomes during cell division. It is epigenetically defined by the presence of the histone H3 variant CENP-A. CENP-A associates specifically with a group of 16 proteins that form the centromere-associated network of proteins (CCAN). In mitosis, the kinetochore forms on the CCAN to connect the duplicated chromosomes to the microtubules protruding from the cell poles. Previous studies have shown that CENP-A replaces H3 in nucleosomes, and recently the structures of CENP-A-containing nucleosomes in complex with CCANs have been revealed, but they show only a limited interaction between CCANs and CENP-A. Here, we report the cryoEM structure of 2x(CENP-A/H4)-di-tetramers assembled on DNA in the absence of H2A/H2B histone dimer and speculate how (CENP-A/H4)-tetramers and -di-tetramers might serve as a platform for CCAN organization.
History
DepositionSep 29, 2024-
Header (metadata) releaseJan 29, 2025-
Map releaseJan 29, 2025-
UpdateJan 29, 2025-
Current statusJan 29, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_51647.png

Downloads & links

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Map

FileDownload / File: emd_51647.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation2x(H3/H4)2 di-tetrasome assembled on alpha-satellite DNA.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 360 pix.
= 295.2 Å		0.82 Å/pix.
x 360 pix.
= 295.2 Å		0.82 Å/pix.
x 360 pix.
= 295.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.82 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0651
Minimum - Maximum-0.1520198 - 0.29813915
Average (Standard dev.)0.0002546524 (±0.0100959325)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 295.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_51647_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_51647_half_map_1.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_51647_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram (log scale)

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Sample components

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Entire : 2x(H3/H4)2 di-tetrasome assembled on alpha-satellite DNA.

EntireName: 2x(H3/H4)2 di-tetrasome assembled on alpha-satellite DNA.
Components
  • Complex: 2x(H3/H4)2 di-tetrasome assembled on alpha-satellite DNA.
    • Protein or peptide: Human H3 histone
    • Protein or peptide: Human H3 histone
    • Protein or peptide: Human H3 histone
    • Protein or peptide: Human H3 histone
    • Protein or peptide: Human H4 histone
    • Protein or peptide: Human H4 histone
    • Protein or peptide: Human H4 histone
    • Protein or peptide: Human H4 histone
    • DNA: Human alpha-satellite DNA
    • DNA: Human alpha-satellite DNA

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Supramolecule #1: 2x(H3/H4)2 di-tetrasome assembled on alpha-satellite DNA.

SupramoleculeName: 2x(H3/H4)2 di-tetrasome 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: Human H3 histone

MacromoleculeName: Human H3 histone / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
SequenceString:
MARTKQTARK STGGKAPRKQ LATKAARKSA PSTGGVKKPH RYRPGTVALR EIRRYQKSTE LLIRKLPFQR LVREIAQDFK TDLRFQSAAI GALQEASEAY LVGLFEDTNL CAIHAKRVTI MPKDIQLARR IRGERA

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Macromolecule #2: Human H3 histone

MacromoleculeName: Human H3 histone / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
SequenceString:
MARTKQTARK STGGKAPRKQ LATKAARKSA PSTGGVKKPH RYRPGTVALR EIRRYQKSTE LLIRKLPFQR LVREIAQDFK TDLRFQSAAI GALQEASEAY LVGLFEDTNL CAIHAKRVTI MPKDIQLARR IRGERA

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Macromolecule #3: Human H3 histone

MacromoleculeName: Human H3 histone / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
SequenceString:
MARTKQTARK STGGKAPRKQ LATKAARKSA PSTGGVKKPH RYRPGTVALR EIRRYQKSTE LLIRKLPFQR LVREIAQDFK TDLRFQSAAI GALQEASEAY LVGLFEDTNL CAIHAKRVTI MPKDIQLARR IRGERA

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Macromolecule #4: Human H3 histone

MacromoleculeName: Human H3 histone / type: protein_or_peptide / ID: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
SequenceString:
MARTKQTARK STGGKAPRKQ LATKAARKSA PSTGGVKKPH RYRPGTVALR EIRRYQKSTE LLIRKLPFQR LVREIAQDFK TDLRFQSAAI GALQEASEAY LVGLFEDTNL CAIHAKRVTI MPKDIQLARR IRGERA

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Macromolecule #5: Human H4 histone

MacromoleculeName: Human H4 histone / type: protein_or_peptide / ID: 5 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
SequenceString:
MSGRGKGGKG LGKGGAKRHR KVLRDNIQGI TKPAIRRLAR RGGVKRISGL IYEETRGVLK VFLENVIRDA VTYTEHAKRK TVTAMDVVYA LKRQGRTLYG FGG

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Macromolecule #6: Human H4 histone

MacromoleculeName: Human H4 histone / type: protein_or_peptide / ID: 6 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
SequenceString:
MSGRGKGGKG LGKGGAKRHR KVLRDNIQGI TKPAIRRLAR RGGVKRISGL IYEETRGVLK VFLENVIRDA VTYTEHAKRK TVTAMDVVYA LKRQGRTLYG FGG

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Macromolecule #7: Human H4 histone

MacromoleculeName: Human H4 histone / type: protein_or_peptide / ID: 7 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
SequenceString:
MSGRGKGGKG LGKGGAKRHR KVLRDNIQGI TKPAIRRLAR RGGVKRISGL IYEETRGVLK VFLENVIRDA VTYTEHAKRK TVTAMDVVYA LKRQGRTLYG FGG

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Macromolecule #8: Human H4 histone

MacromoleculeName: Human H4 histone / type: protein_or_peptide / ID: 8 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
SequenceString:
MSGRGKGGKG LGKGGAKRHR KVLRDNIQGI TKPAIRRLAR RGGVKRISGL IYEETRGVLK VFLENVIRDA VTYTEHAKRK TVTAMDVVYA LKRQGRTLYG FGG

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Macromolecule #9: Human alpha-satellite DNA

MacromoleculeName: Human alpha-satellite DNA / type: dna / ID: 9 / Classification: DNA
Source (natural)Organism: Homo sapiens (human)
SequenceString:
ATCAAATATC CACCTGCAGA TTCTACCAAA AGTGTATTTG GAAACTGCTC CATCAAAAGG CATGTTCAGC TCTGTGAGTG AAACTCCATC ATCA CAAAG AATATTCTGA GAATGCTTCC GTTTGCCTTT TATATGAACT TCCTCGAT

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Macromolecule #10: Human alpha-satellite DNA

MacromoleculeName: Human alpha-satellite DNA / type: dna / ID: 10 / Classification: DNA
Source (natural)Organism: Homo sapiens (human)
SequenceString:
ATCGAGGAAG TTCATATAAA AGGCAAACGG AAGCATTCTC AGAATATTCT TTGTGATGAT GGAGTTTCAC TCACAGAGCT GAACATGCCT TTTG ATGGA GCAGTTTCCA AATACACTTT TGGTAGAATC TGCAGGTGGA TATTTGAT

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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

BufferpH: 7.5 / Component:
ConcentrationName
10.0 mMTris
100.0 mMNaCl
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 279 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k 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 / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 158300
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.75 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 64700
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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