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- EMDB-18763: Human CENP-A nucleosome assembled on alpha-satellite DNA in compl... -

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Basic information

Entry
Database: EMDB / ID: EMD-18763
TitleHuman CENP-A nucleosome assembled on alpha-satellite DNA in complex with CENP-B (partially unwrapped DNA)
Map dataHuman CENP-A nucleosome assembled on alpha-satellite DNA in complex with CENP-B (partially unwrapped DNA)
Sample
  • Complex: Human CENP-A nucleosome assembled on alpha-satellite DNA in complex with CENP-B (partially 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
    • Protein or peptide: Human CENP-B
    • DNA: Human alpha-satellite DNA
KeywordsNucleosome / centromere / centromeric / CENP-A / Histones / Human / DNA / DNA BINDING PROTEIN
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 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 26, 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_18763.png

Downloads & links

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Map

FileDownload / File: emd_18763.map.gz / Format: CCP4 / Size: 15.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationHuman CENP-A nucleosome assembled on alpha-satellite DNA in complex with CENP-B (partially unwrapped DNA)
Projections & slices

Image control

Size
Brightness
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AxesZ (Sec.)Y (Row.)X (Col.)
1.58 Å/pix.
x 160 pix.
= 253.44 Å		1.58 Å/pix.
x 160 pix.
= 253.44 Å		1.58 Å/pix.
x 160 pix.
= 253.44 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.584 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.102
Minimum - Maximum-0.33498794 - 0.62340736
Average (Standard dev.)0.0019259125 (±0.026691472)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions160160160
Spacing160160160
CellA=B=C: 253.44 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_18763_msk_1.map
Projections & Slices
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Half map: #2

Fileemd_18763_half_map_1.map
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Half map: #1

Fileemd_18763_half_map_2.map
Projections & Slices
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Sample components

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Entire : Human CENP-A nucleosome assembled on alpha-satellite DNA in compl...

EntireName: Human CENP-A nucleosome assembled on alpha-satellite DNA in complex with CENP-B (partially unwrapped DNA)
Components
  • Complex: Human CENP-A nucleosome assembled on alpha-satellite DNA in complex with CENP-B (partially 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
    • Protein or peptide: Human CENP-B
    • DNA: Human alpha-satellite DNA

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Supramolecule #1: Human CENP-A nucleosome assembled on alpha-satellite DNA in compl...

SupramoleculeName: Human CENP-A nucleosome assembled on alpha-satellite DNA in complex with CENP-B (partially 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)
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)
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 CENP-B

MacromoleculeName: Human CENP-B / type: protein_or_peptide / ID: 5 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
SequenceString: DSLEFIASKL AGPKRRQLTF REKSRIIQEV EENPDLRKGE IARRFNIPPS TLSTILKNKR AILASERKYG VASTCRKTNK LSPYDKLEGL LIAWFQQIRA AGLPVKGIIL KEKALRIAEE LGMDDFTASN GWLDRFRRRH GVVSCSGVAR ARARNAAPRT PAAPASPAAV ...String:
DSLEFIASKL AGPKRRQLTF REKSRIIQEV EENPDLRKGE IARRFNIPPS TLSTILKNKR AILASERKYG VASTCRKTNK LSPYDKLEGL LIAWFQQIRA AGLPVKGIIL KEKALRIAEE LGMDDFTASN GWLDRFRRRH GVVSCSGVAR ARARNAAPRT PAAPASPAAV PSEGSGGSTT GWRAREEQPP SVAEGYASQD VFSATETSLW YDFLPDQAAG LCGGDGRPRQ ATQRLSVLLC ANADGSEKLP PLVAGKSAKP RAGQAGLPCD YTANSKGGVT TQALAKYLKA LDTRMAAESR RVLLLAGRLA AQSLDTSGLR HVQLAFFPPG TVHPLERGVV QQVKGHYRQA MLLKAMAALE GQDPSGLQLG LTEALHFVAA AWQAVEPSDI AACFREAGFG GGPNATITTS LKSEGEEEEE EEEEEEEEEG EGEEEEEEGE EEEEEGGEGE ELGEEEEVEE EGDVDSDEEE EEDEESSSEG LEAEDWAQGV VEAGGSFGAY GAQEEAQCPT LHFLEGGEDS DSDSEEEDDE EEDDEDEDDD DDEEDGDEVP VPSFGEAMAY FAMVKRYLTS FPIDDRVQSH ILHLEHDLVH VTRKNHARQA GVRGLGHQSP HHHHHH

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Macromolecule #6: Human alpha-satellite DNA

MacromoleculeName: Human alpha-satellite DNA / type: dna / ID: 6 / 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

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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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

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 101005
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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