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Yorodumi- EMDB-18753: Human CENP-A nucleosome assembled on alpha-satellite DNA in compl... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-18753 | |||||||||
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Title | Human CENP-A nucleosome assembled on alpha-satellite DNA in complex with CENP-B (most wrapped DNA) | |||||||||
Map data | Human CENP-A nucleosome assembled on alpha-satellite DNA in complex with CENP-B (most wrapped DNA) | |||||||||
Sample |
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Keywords | Nucleosome / centromere / centromeric / CENP-A / Histones / Human / DNA / DNA BINDING PROTEIN | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.5 Å | |||||||||
Authors | Ali-Ahmad A / Sekulic N | |||||||||
Funding support | Norway, 2 items
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Citation | Journal: 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 |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_18753.map.gz | 8 MB | EMDB map data format | |
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Header (meta data) | emd-18753-v30.xml emd-18753.xml | 17.8 KB 17.8 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_18753_fsc.xml | 5.2 KB | Display | FSC data file |
Images | emd_18753.png | 36.4 KB | ||
Masks | emd_18753_msk_1.map | 15.6 MB | Mask map | |
Filedesc metadata | emd-18753.cif.gz | 5.3 KB | ||
Others | emd_18753_half_map_1.map.gz emd_18753_half_map_2.map.gz | 14.5 MB 14.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-18753 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-18753 | HTTPS FTP |
-Validation report
Summary document | emd_18753_validation.pdf.gz | 1 MB | Display | EMDB validaton report |
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Full document | emd_18753_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | emd_18753_validation.xml.gz | 12.1 KB | Display | |
Data in CIF | emd_18753_validation.cif.gz | 15.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-18753 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-18753 | HTTPS FTP |
-Related structure data
Related structure data | C: citing same article (ref.) |
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-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_18753.map.gz / Format: CCP4 / Size: 15.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | Human CENP-A nucleosome assembled on alpha-satellite DNA in complex with CENP-B (most wrapped DNA) | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.584 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_18753_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_18753_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_18753_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Human CENP-A nucleosome assembled on alpha-satellite DNA in compl...
Entire | Name: Human CENP-A nucleosome assembled on alpha-satellite DNA in complex with CENP-B (most wrapped DNA) |
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Components |
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-Supramolecule #1: Human CENP-A nucleosome assembled on alpha-satellite DNA in compl...
Supramolecule | Name: Human CENP-A nucleosome assembled on alpha-satellite DNA in complex with CENP-B (most wrapped DNA) type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Homo sapiens (human) |
-Macromolecule #1: Human histone CENP-A
Macromolecule | Name: Human histone CENP-A / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MARTKQTARK STGGKAPRKQ LATKAARKSA PATGGVKKPH RYRPGTVALR EIRKLQKSTH LLIRKLPFSR LAREICVKFT RGVDFNWQAQ ALLALQEAAE AFLVHLFEDA YLLTLHAGRV TLFPKDVQLA RRIRGLEEGL G |
-Macromolecule #2: Human histone H4
Macromolecule | Name: Human histone H4 / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MSGRGKGGKG LGKGGAKRHR KVLRDNIQGI TKPAIRRLAR RGGVKRISGL IYEETRGVLK VFLENVIRDA VTYTEHAKRK TVTAMDVVYA LKRQGRTLYG FGG |
-Macromolecule #3: Human histone H2A
Macromolecule | Name: Human histone H2A / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: GPLGMSGRGK QGGKARAKAK SRSSRAGLQF PVGRVHRLLR KGNYAERVGA GAPVYMAAVL EYLTAEILEL AGNAARDNKK TRIIPRHLQL AIRNDEELNK LLGKVTIAQG GVLPNIQAVL LPKKTESHHK AKGK |
-Macromolecule #4: Human histone H2B
Macromolecule | Name: Human histone H2B / type: protein_or_peptide / ID: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MPEPAKSAPA PKKGSKKAVT KAQKKDGKKR KRSRKESYSV YVYKVLKQVH PDTGISSKAM GIMNSFVNDI FERIAGEASR LAHYNKRSTI TSREIQTAVR LLLPGELAKH AVSEGTKAVT KYTSSK |
-Macromolecule #5: Human CENP-B
Macromolecule | Name: Human CENP-B / type: protein_or_peptide / ID: 5 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: 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 |
-Macromolecule #6: Human alpha-satellite DNA
Macromolecule | Name: Human alpha-satellite DNA / type: protein_or_peptide / ID: 6 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Sequence | String: GGAGGATTTC GTTGGAAACG GGATCAACTT CCCATAACTG AACGGAAGCA AACTCAGAAC ATTCTTTGTG ATGTTTGTAT TCAACTCACA GAGTTGAACC TTCCTTTGAT AGTTCAGGTT TGCAACACCC TTGTAGTAGA ATCTGCAAGT GTATATTTTG ACCACTTTGG A |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination 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 |