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Yorodumi- EMDB-9127: A nucleosome bridging mechanism for activation of a maintenance D... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-9127 | |||||||||
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Title | A nucleosome bridging mechanism for activation of a maintenance DNA methyltransferase | |||||||||
Map data | Negative stain map of ZMET2 in complex with H3Kc9me3 dinucleosome with 20 pase pairs of linker DNA. | |||||||||
Sample |
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Biological species | Xenopus laevis (African clawed frog) / Zea mays (maize) / synthetic construct (others) | |||||||||
Method | single particle reconstruction / negative staining / Resolution: 28.0 Å | |||||||||
Authors | Stoddard CI / Feng S / Campbell MG / Liu W / Wang H / Zhong X / Bernatavichute Y / Cheng Y / Jacobsen SE / Narlikar GJ | |||||||||
Citation | Journal: Mol Cell / Year: 2019 Title: A Nucleosome Bridging Mechanism for Activation of a Maintenance DNA Methyltransferase. Authors: Caitlin I Stoddard / Suhua Feng / Melody G Campbell / Wanlu Liu / Haifeng Wang / Xuehua Zhong / Yana Bernatavichute / Yifan Cheng / Steven E Jacobsen / Geeta J Narlikar / Abstract: DNA methylation and H3K9me are hallmarks of heterochromatin in plants and mammals, and are successfully maintained across generations. The biochemical and structural basis for this maintenance is ...DNA methylation and H3K9me are hallmarks of heterochromatin in plants and mammals, and are successfully maintained across generations. The biochemical and structural basis for this maintenance is poorly understood. The maintenance DNA methyltransferase from Zea mays, ZMET2, recognizes dimethylation of H3K9 via a chromodomain (CD) and a bromo adjacent homology (BAH) domain, which flank the catalytic domain. Here, we show that dinucleosomes are the preferred ZMET2 substrate, with DNA methylation preferentially targeted to linker DNA. Electron microscopy shows one ZMET2 molecule bridging two nucleosomes within a dinucleosome. We find that the CD stabilizes binding, whereas the BAH domain enables allosteric activation by the H3K9me mark. ZMET2 further couples recognition of H3K9me to an increase in the specificity for hemimethylated versus unmethylated DNA. We propose a model in which synergistic coupling between recognition of nucleosome spacing, H3K9 methylation, and DNA modification allows ZMET2 to maintain DNA methylation in heterochromatin with high fidelity. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_9127.map.gz | 1.9 MB | EMDB map data format | |
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Header (meta data) | emd-9127-v30.xml emd-9127.xml | 10 KB 10 KB | Display Display | EMDB header |
Images | emd_9127.png | 21 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-9127 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-9127 | HTTPS FTP |
-Validation report
Summary document | emd_9127_validation.pdf.gz | 78.8 KB | Display | EMDB validaton report |
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Full document | emd_9127_full_validation.pdf.gz | 78 KB | Display | |
Data in XML | emd_9127_validation.xml.gz | 494 B | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-9127 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-9127 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_9127.map.gz / Format: CCP4 / Size: 3.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Negative stain map of ZMET2 in complex with H3Kc9me3 dinucleosome with 20 pase pairs of linker DNA. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 3.14 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Complex of ZMET2 with H3Kc9me3 dinucleosome with 20 base pairs of...
Entire | Name: Complex of ZMET2 with H3Kc9me3 dinucleosome with 20 base pairs of linker DNA. |
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Components |
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-Supramolecule #1: Complex of ZMET2 with H3Kc9me3 dinucleosome with 20 base pairs of...
Supramolecule | Name: Complex of ZMET2 with H3Kc9me3 dinucleosome with 20 base pairs of linker DNA. type: complex / ID: 1 / Parent: 0 |
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-Supramolecule #2: Xenopus histones
Supramolecule | Name: Xenopus histones / type: complex / ID: 2 / Parent: 1 |
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Source (natural) | Organism: Xenopus laevis (African clawed frog) |
Recombinant expression | Organism: Escherichia coli (E. coli) |
-Supramolecule #3: ZMET2
Supramolecule | Name: ZMET2 / type: complex / ID: 3 / Parent: 1 |
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Source (natural) | Organism: Zea mays (maize) |
Recombinant expression | Organism: Escherichia coli (E. coli) |
-Supramolecule #4: 601 dinucleosomal DNA
Supramolecule | Name: 601 dinucleosomal DNA / type: complex / ID: 4 / Parent: 1 |
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Source (natural) | Organism: synthetic construct (others) |
Recombinant expression | Organism: Escherichia coli (E. coli) |
-Experimental details
-Structure determination
Method | negative staining |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 |
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Staining | Type: NEGATIVE / Material: Uranyl Formate |
Grid | Details: unspecified |
-Electron microscopy
Microscope | FEI TECNAI 20 |
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Image recording | Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Average electron dose: 20.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: LAB6 |
Electron optics | Illumination mode: OTHER / Imaging mode: BRIGHT FIELD |