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- EMDB-51656: CENP-A/H4 tetra-tetrasome assembled on 342 bp alpha-satellite DNA. -

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Basic information

Entry
Database: EMDB / ID: EMD-51656
TitleCENP-A/H4 tetra-tetrasome assembled on 342 bp alpha-satellite DNA.
Map data4x(CENP-A/H4)2 tetra-tetramer assembled on 342 bp alpha-satellite DNA
Sample
  • Complex: 2x(H3/H4)2 di-tetrasome assembled on alpha-satellite DNA.
    • Protein or peptide: Human CENP-A histone
  • Protein or peptide: Human H4 histone
  • DNA: Human alpha-satellite DNA
  • DNA: human alpha-satellite DNA
KeywordsCENP-A/H4 / di-tetrasome / nucleosome / centromere / CENP-A / Human / Cell division. / DNA BINDING PROTEIN
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 7.01 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_51656.png

Downloads & links

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Map

FileDownload / File: emd_51656.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation4x(CENP-A/H4)2 tetra-tetramer assembled on 342 bp alpha-satellite DNA
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.31 Å/pix.
x 280 pix.
= 366.072 Å		1.31 Å/pix.
x 280 pix.
= 366.072 Å		1.31 Å/pix.
x 280 pix.
= 366.072 Å

Surface

Projections

Slices (1/3)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.3074 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0887
Minimum - Maximum-0.079192095 - 0.32723993
Average (Standard dev.)0.0011492008 (±0.011214694)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 366.072 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_51656_msk_1.map
Projections & Slices
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Half map: #1

Fileemd_51656_half_map_1.map
Projections & Slices
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Histogram

Histogram (log scale)

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Half map: #2

Fileemd_51656_half_map_2.map
Projections & Slices
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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 CENP-A 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: #1
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Human CENP-A histone

MacromoleculeName: Human CENP-A histone / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
SequenceString:
MGPRRRSRKP EAPRRRSPSP TPTPGPSRRG PSLGASSHQH SRRRQGWLKE IRKLQKSTHL LIRKLPFSRL AREICVKFTR GVDFNWQAQA LLALQEAAEA FLVHLFEDAY LLTLHAGRVT LFPKDVQLAR RIRGLEEGLG

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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)
SequenceString:
MSGRGKGGKG LGKGGAKRHR KVLRDNIQGI TKPAIRRLAR RGGVKRISGL IYEETRGVLK VFLENVIRDA VTYTEHAKRK TVTAMDVVYA LKRQGRTLYG FGG

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Macromolecule #3: Human alpha-satellite DNA

MacromoleculeName: Human alpha-satellite DNA / type: dna / ID: 3 / Classification: DNA
Source (natural)Organism: Homo sapiens (human)
SequenceString: GGTACCTGAG GCCTGTGGTA GTAAAGGAAA GAACTTCATA TAAAAACTAG ACGGTAGCAC CCTCAGAAAA TTCTTTGTGA CGATGGAGTT TAACTCAGAG AG CTGAACA TTCGTTATGA TGGAGCAGTT TCCAAACACA CGTTTTGTAG AATCTGCAAG GGGATATTTG ...String:
GGTACCTGAG GCCTGTGGTA GTAAAGGAAA GAACTTCATA TAAAAACTAG ACGGTAGCAC CCTCAGAAAA TTCTTTGTGA CGATGGAGTT TAACTCAGAG AG CTGAACA TTCGTTATGA TGGAGCAGTT TCCAAACACA CGTTTTGTAG AATCTGCAAG GGGATATTTG GACCTTCCGG AGGATTTCGT TGGAAACGGG ATCAA CTTC CCATAACTGA ACGGAAGCAA ACTCAGAACA TTCTTTGTGA TGTTTGTATT CAACTCACAG AGTTGAACCT TCCTTTGATA GTTCAGGTTT GCAACACC C TTGTAGTAGA ATCTGCAAGT GTATATTTTG ACCAC

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Macromolecule #4: human alpha-satellite DNA

MacromoleculeName: human alpha-satellite DNA / type: dna / ID: 4 / Classification: DNA
Source (natural)Organism: Homo sapiens (human)
SequenceString: GTGGTCAAAA TATACACTTG CAGATTCTAC TACAAGGGTG TTGCAAACCT GAACTATCAA AGGAAGGTTC AACTCTGTGA GTTGAATACA AACATCACAA AGAATGTTCT GAGTTTGCTT CCGTTCAGTT ATGGGAAGTT GATCCCGTTT CCAACGAAAT CCTCCGGAAG ...String:
GTGGTCAAAA TATACACTTG CAGATTCTAC TACAAGGGTG TTGCAAACCT GAACTATCAA AGGAAGGTTC AACTCTGTGA GTTGAATACA AACATCACAA AGAATGTTCT GAGTTTGCTT CCGTTCAGTT ATGGGAAGTT GATCCCGTTT CCAACGAAAT CCTCCGGAAG GTCCAAATAT CCCCTTGCAG ATTCTACAAA ACGTGTGTTT GGAAACTGCT CCATCATAAC GAATGTTCAG CTCTCTGAGT TAAACTCCAT CGTCACAAAG AATTTTCTGA GGGTGCTACC GTCTAGTTTT TATATGAAGT TCTTTCCTTT ACTACCACAG GCCTCAGGTA CC

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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: 76800
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 7.01 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 27000
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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