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Yorodumi- EMDB-18699: Human H3 nucleosome assembled on alpha-satellite DNA (Class1: mos... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-18699 | |||||||||
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Title | Human H3 nucleosome assembled on alpha-satellite DNA (Class1: most wrapped DNA) | |||||||||
Map data | Human H3 nucleosome assembled on aplha-satellite DNA | |||||||||
Sample |
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Keywords | Nucleosome / canonical / H3 / Histones / Human / DNA / DNA BINDING PROTEIN | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.73 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_18699.map.gz | 88.7 MB | EMDB map data format | |
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Header (meta data) | emd-18699-v30.xml emd-18699.xml | 17.2 KB 17.2 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_18699_fsc.xml | 11.9 KB | Display | FSC data file |
Images | emd_18699.png | 68.7 KB | ||
Masks | emd_18699_msk_1.map | 178 MB | Mask map | |
Filedesc metadata | emd-18699.cif.gz | 5.2 KB | ||
Others | emd_18699_half_map_1.map.gz emd_18699_half_map_2.map.gz | 165.1 MB 165.1 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-18699 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-18699 | HTTPS FTP |
-Validation report
Summary document | emd_18699_validation.pdf.gz | 955 KB | Display | EMDB validaton report |
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Full document | emd_18699_full_validation.pdf.gz | 954.6 KB | Display | |
Data in XML | emd_18699_validation.xml.gz | 20.6 KB | Display | |
Data in CIF | emd_18699_validation.cif.gz | 26.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-18699 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-18699 | 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_18699.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | Human H3 nucleosome assembled on aplha-satellite DNA | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.704 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_18699_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_18699_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_18699_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Human H3 nucleosome assembled on alpha-satellite DNA
Entire | Name: Human H3 nucleosome assembled on alpha-satellite DNA |
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Components |
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-Supramolecule #1: Human H3 nucleosome assembled on alpha-satellite DNA
Supramolecule | Name: Human H3 nucleosome assembled on alpha-satellite DNA / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Homo sapiens (human) |
-Macromolecule #1: H3 histone
Macromolecule | Name: H3 histone / 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: GSMARTKQTA RKSTGGKAPR KQLATKAARK SAPSTGGVKK PHRYRPGTVA LREIRRYQKS TELLIRKLPF QRLVREIAQD FKTDLRFQSA AIGALQEASE AYLVGLFEDT NLCAIHAKRV TIMPKDIQLA RRIRGERA |
-Macromolecule #2: H4 histone
Macromolecule | Name: H4 histone / 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: GSMSGRGKGG KGLGKGGAKR HRKVLRDNIQ GITKPAIRRL ARRGGVKRIS GLIYEETRGV LKVFLENVIR DAVTYTEHAK RKTVTAMDVV YALKRQGRTL YGFGG |
-Macromolecule #3: H2A histone
Macromolecule | Name: H2A histone / 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: SGMKETAAAK FERQHMDSPD LGTLEVLFQG PLGMSGRGKQ GGKARAKAKS RSSRAGLQFP VGRVHRLLRK GNYAERVGAG APVYMAAVLE YLTAEILELA GNAARDNKKT RIIPRHLQLA IRNDEELNKL LGKVTIAQGG VLPNIQAVLL PKKTESHHKA KGK |
-Macromolecule #4: H2B histone
Macromolecule | Name: H2B histone / 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: alpha-satellite DNA
Macromolecule | Name: alpha-satellite DNA / type: dna / ID: 5 / Classification: DNA |
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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
Concentration | 1.1 mg/mL |
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Buffer | pH: 7.5 |
Grid | Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 45 sec. |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 6 K / Instrument: FEI VITROBOT MARK IV |
-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 |