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- EMDB-51645: CENP-A/H4 di-tetrasome assembled on alpha-satellite DNA. -

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Basic information

Entry
Database: EMDB / ID: EMD-51645
TitleCENP-A/H4 di-tetrasome assembled on alpha-satellite DNA.
Map data2x(CENP-A/H4)2 di-tetrasome assembled on 147bp alpha-satellite DNA.
Sample
  • Complex: 2x(CENP-A/H4)2 di-tetrasome assembled on alpha-satellite DNA.
    • Protein or peptide: Histone H3-like centromeric protein A
    • Protein or peptide: Histone H4
    • DNA: 147 bp human alpha-satellite DNA
    • DNA: 147 bp alpha-satellite DNA
KeywordsCENP-A/H4 / di-tetrasome / nucleosome / centromere / CENP-A / Human / Cell division. / DNA BINDING PROTEIN
Function / homology
Function and homology information


CENP-A containing chromatin assembly / kinetochore assembly / protein localization to chromosome, centromeric region / condensed chromosome, centromeric region / establishment of mitotic spindle orientation / mitotic cytokinesis / chromosome, centromeric region / negative regulation of megakaryocyte differentiation / protein localization to CENP-A containing chromatin / pericentric heterochromatin ...CENP-A containing chromatin assembly / kinetochore assembly / protein localization to chromosome, centromeric region / condensed chromosome, centromeric region / establishment of mitotic spindle orientation / mitotic cytokinesis / chromosome, centromeric region / negative regulation of megakaryocyte differentiation / protein localization to CENP-A containing chromatin / pericentric heterochromatin / Replacement of protamines by nucleosomes in the male pronucleus / CENP-A containing nucleosome / Packaging Of Telomere Ends / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / Deposition of new CENPA-containing nucleosomes at the centromere / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / telomere organization / Inhibition of DNA recombination at telomere / Meiotic synapsis / RNA Polymerase I Promoter Opening / Assembly of the ORC complex at the origin of replication / Resolution of Sister Chromatid Cohesion / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / SUMOylation of chromatin organization proteins / DNA methylation / Condensation of Prophase Chromosomes / Chromatin modifications during the maternal to zygotic transition (MZT) / HCMV Late Events / SIRT1 negatively regulates rRNA expression / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / PRC2 methylates histones and DNA / Regulation of endogenous retroelements by KRAB-ZFP proteins / Defective pyroptosis / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / HDACs deacetylate histones / Nonhomologous End-Joining (NHEJ) / RNA Polymerase I Promoter Escape / Transcriptional regulation by small RNAs / RHO GTPases Activate Formins / Formation of the beta-catenin:TCF transactivating complex / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / G2/M DNA damage checkpoint / HDMs demethylate histones / NoRC negatively regulates rRNA expression / DNA Damage/Telomere Stress Induced Senescence / B-WICH complex positively regulates rRNA expression / PKMTs methylate histone lysines / Meiotic recombination / Pre-NOTCH Transcription and Translation / RMTs methylate histone arginines / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Transcriptional regulation of granulopoiesis / HCMV Early Events / structural constituent of chromatin / Separation of Sister Chromatids / nucleosome / nucleosome assembly / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / chromatin organization / HATs acetylate histones / RUNX1 regulates transcription of genes involved in differentiation of HSCs / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / Processing of DNA double-strand break ends / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / chromosome, telomeric region / Amyloid fiber formation / protein heterodimerization activity / chromatin binding / protein-containing complex / DNA binding / RNA binding / extracellular exosome / extracellular region / nucleoplasm / nucleus / membrane / cytosol
Similarity search - Function
TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / Histone H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / Histone H3 signature 2. / Histone H3 ...TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / Histone H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Histone-fold
Similarity search - Domain/homology
Histone H3-like centromeric protein A / Histone H4
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.01 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_51645.png

Downloads & links

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Map

FileDownload / File: emd_51645.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation2x(CENP-A/H4)2 di-tetrasome assembled on 147bp 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: 0.108
Minimum - Maximum-0.13940057 - 0.33944777
Average (Standard dev.)0.0001283889 (±0.011302969)
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_51645_msk_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Half map: #1

Fileemd_51645_half_map_1.map
Projections & Slices
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Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_51645_half_map_2.map
Projections & Slices
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Histogram (log scale)

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Sample components

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

EntireName: 2x(CENP-A/H4)2 di-tetrasome assembled on alpha-satellite DNA.
Components
  • Complex: 2x(CENP-A/H4)2 di-tetrasome assembled on alpha-satellite DNA.
    • Protein or peptide: Histone H3-like centromeric protein A
    • Protein or peptide: Histone H4
    • DNA: 147 bp human alpha-satellite DNA
    • DNA: 147 bp alpha-satellite DNA

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

SupramoleculeName: 2x(CENP-A/H4)2 di-tetrasome assembled on alpha-satellite DNA.
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 200 kDa/nm

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Macromolecule #1: Histone H3-like centromeric protein A

MacromoleculeName: Histone H3-like centromeric protein A / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 15.892434 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
GPRRRSRKPE APRRRSPSPT PTPGPSRRGP SLGASSHQHS RRRQGWLKEI RKLQKSTHLL IRKLPFSRLA REICVKFTRG VDFNWQAQA LLALQEAAEA FLVHLFEDAY LLTLHAGRVT LFPKDVQLAR RIRGLEEGLG

UniProtKB: Histone H3-like centromeric protein A

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Macromolecule #2: Histone H4

MacromoleculeName: Histone H4 / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.263231 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
SGRGKGGKGL GKGGAKRHRK VLRDNIQGIT KPAIRRLARR GGVKRISGLI YEETRGVLKV FLENVIRDAV TYTEHAKRKT VTAMDVVYA LKRQGRTLYG FGG

UniProtKB: Histone H4

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Macromolecule #3: 147 bp human alpha-satellite DNA

MacromoleculeName: 147 bp human alpha-satellite DNA / type: dna / ID: 3 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 45.141918 KDa
SequenceString: (DA)(DT)(DC)(DA)(DA)(DA)(DT)(DA)(DT)(DC) (DC)(DA)(DC)(DC)(DT)(DG)(DC)(DA)(DG)(DA) (DT)(DT)(DC)(DT)(DA)(DC)(DC)(DA)(DA) (DA)(DA)(DG)(DT)(DG)(DT)(DA)(DT)(DT)(DT) (DG) (DG)(DA)(DA)(DA)(DC)(DT) ...String:
(DA)(DT)(DC)(DA)(DA)(DA)(DT)(DA)(DT)(DC) (DC)(DA)(DC)(DC)(DT)(DG)(DC)(DA)(DG)(DA) (DT)(DT)(DC)(DT)(DA)(DC)(DC)(DA)(DA) (DA)(DA)(DG)(DT)(DG)(DT)(DA)(DT)(DT)(DT) (DG) (DG)(DA)(DA)(DA)(DC)(DT)(DG)(DC) (DT)(DC)(DC)(DA)(DT)(DC)(DA)(DA)(DA)(DA) (DG)(DG) (DC)(DA)(DT)(DG)(DT)(DT)(DC) (DA)(DG)(DC)(DT)(DC)(DT)(DG)(DT)(DG)(DA) (DG)(DT)(DG) (DA)(DA)(DA)(DC)(DT)(DC) (DC)(DA)(DT)(DC)(DA)(DT)(DC)(DA)(DC)(DA) (DA)(DA)(DG)(DA) (DA)(DT)(DA)(DT)(DT) (DC)(DT)(DG)(DA)(DG)(DA)(DA)(DT)(DG)(DC) (DT)(DT)(DC)(DC)(DG) (DT)(DT)(DT)(DG) (DC)(DC)(DT)(DT)(DT)(DT)(DA)(DT)(DA)(DT) (DG)(DA)(DA)(DC)(DT)(DT) (DC)(DC)(DT) (DC)(DG)(DA)(DT)

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Macromolecule #4: 147 bp alpha-satellite DNA

MacromoleculeName: 147 bp alpha-satellite DNA / type: dna / ID: 4 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 45.582188 KDa
SequenceString: (DA)(DT)(DC)(DG)(DA)(DG)(DG)(DA)(DA)(DG) (DT)(DT)(DC)(DA)(DT)(DA)(DT)(DA)(DA)(DA) (DA)(DG)(DG)(DC)(DA)(DA)(DA)(DC)(DG) (DG)(DA)(DA)(DG)(DC)(DA)(DT)(DT)(DC)(DT) (DC) (DA)(DG)(DA)(DA)(DT)(DA) ...String:
(DA)(DT)(DC)(DG)(DA)(DG)(DG)(DA)(DA)(DG) (DT)(DT)(DC)(DA)(DT)(DA)(DT)(DA)(DA)(DA) (DA)(DG)(DG)(DC)(DA)(DA)(DA)(DC)(DG) (DG)(DA)(DA)(DG)(DC)(DA)(DT)(DT)(DC)(DT) (DC) (DA)(DG)(DA)(DA)(DT)(DA)(DT)(DT) (DC)(DT)(DT)(DT)(DG)(DT)(DG)(DA)(DT)(DG) (DA)(DT) (DG)(DG)(DA)(DG)(DT)(DT)(DT) (DC)(DA)(DC)(DT)(DC)(DA)(DC)(DA)(DG)(DA) (DG)(DC)(DT) (DG)(DA)(DA)(DC)(DA)(DT) (DG)(DC)(DC)(DT)(DT)(DT)(DT)(DG)(DA)(DT) (DG)(DG)(DA)(DG) (DC)(DA)(DG)(DT)(DT) (DT)(DC)(DC)(DA)(DA)(DA)(DT)(DA)(DC)(DA) (DC)(DT)(DT)(DT)(DT) (DG)(DG)(DT)(DA) (DG)(DA)(DA)(DT)(DC)(DT)(DG)(DC)(DA)(DG) (DG)(DT)(DG)(DG)(DA)(DT) (DA)(DT)(DT) (DT)(DG)(DA)(DT)

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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
GridModel: Quantifoil R2/1 / Material: COPPER / Support film - Material: GRAPHENE OXIDE
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: 119300
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.01 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 22500
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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