+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-6837 | ||||||||||||
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Title | Human HP1gamma-dinucleosome H3K9Me3 | ||||||||||||
Map data | HP1gamma dinucleosome-H3K9me3 complex | ||||||||||||
Sample |
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Biological species | Homo sapiens (human) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 24.0 Å | ||||||||||||
Authors | Machida S / Takizawa Y / Ishimaru M / Sekine S / Sugita Y / Nakayama J / Wolf M / Kurumizaka H | ||||||||||||
Funding support | Japan, 3 items
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Citation | Journal: Mol Cell / Year: 2018 Title: Structural Basis of Heterochromatin Formation by Human HP1. Authors: Shinichi Machida / Yoshimasa Takizawa / Masakazu Ishimaru / Yukihiko Sugita / Satoshi Sekine / Jun-Ichi Nakayama / Matthias Wolf / Hitoshi Kurumizaka / Abstract: Heterochromatin plays important roles in transcriptional silencing and genome maintenance by the formation of condensed chromatin structures, which determine the epigenetic status of eukaryotic cells. ...Heterochromatin plays important roles in transcriptional silencing and genome maintenance by the formation of condensed chromatin structures, which determine the epigenetic status of eukaryotic cells. The trimethylation of histone H3 lysine 9 (H3K9me3), a target of heterochromatin protein 1 (HP1), is a hallmark of heterochromatin formation. However, the mechanism by which HP1 folds chromatin-containing H3K9me3 into a higher-order structure has not been elucidated. Here we report the three-dimensional structure of the H3K9me3-containing dinucleosomes complexed with human HP1α, HP1β, and HP1γ, determined by cryogenic electron microscopy with a Volta phase plate. In the structures, two H3K9me3 nucleosomes are bridged by a symmetric HP1 dimer. Surprisingly, the linker DNA between the nucleosomes does not directly interact with HP1, thus allowing nucleosome remodeling by the ATP-utilizing chromatin assembly and remodeling factor (ACF). The structure depicts the fundamental architecture of heterochromatin. | ||||||||||||
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_6837.map.gz | 20 MB | EMDB map data format | |
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Header (meta data) | emd-6837-v30.xml emd-6837.xml | 16.2 KB 16.2 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_6837_fsc.xml | 9.3 KB | Display | FSC data file |
Images | emd_6837.png | 30 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-6837 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-6837 | HTTPS FTP |
-Validation report
Summary document | emd_6837_validation.pdf.gz | 78.6 KB | Display | EMDB validaton report |
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Full document | emd_6837_full_validation.pdf.gz | 77.7 KB | Display | |
Data in XML | emd_6837_validation.xml.gz | 495 B | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-6837 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-6837 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_6837.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | HP1gamma dinucleosome-H3K9me3 complex | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.4 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 : Human HP1gamma-dinucleosome H3K9Me3 complex
Entire | Name: Human HP1gamma-dinucleosome H3K9Me3 complex |
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Components |
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-Supramolecule #1: Human HP1gamma-dinucleosome H3K9Me3 complex
Supramolecule | Name: Human HP1gamma-dinucleosome H3K9Me3 complex / type: complex / ID: 1 / Parent: 0 |
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Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Escherichia coli (E. coli) Recombinant plasmid: pH2A, pH2B, pH3.2K9C/C110A, pH4, pHP1g-pre |
Molecular weight | Theoretical: 500 KDa |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | .8 mg/mL | |||||||||
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Buffer | pH: 7.5 Component:
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Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 100.0 nm / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Atmosphere: OTHER / Pretreatment - Pressure: 9.33 kPa / Details: Gatan Solarus | |||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 289 K / Instrument: FEI VITROBOT MARK IV / Details: 3 second blot, 2.5uL. | |||||||||
Details | sample was monodisperse |
-Electron microscopy
Microscope | FEI TALOS ARCTICA |
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Temperature | Min: 77.0 K / Max: 100.0 K |
Alignment procedure | Coma free - Residual tilt: 0.1 mrad |
Specialist optics | Phase plate: VOLTA PHASE PLATE |
Details | nanoprobe, parallel beam illumination |
Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Digitization - Sampling interval: 14.0 µm / Digitization - Frames/image: 1-40 / Number grids imaged: 1 / Number real images: 3010 / Average exposure time: 1.0 sec. / Average electron dose: 67.0 e/Å2 Details: Images were collected with a volta phase plate (VPP) at a target defocus of -500nm |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 50.0 µm / Calibrated defocus max: -0.5 µm / Calibrated defocus min: -0.5 µm / Calibrated magnification: 100000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: -0.5 µm / Nominal defocus min: -0.5 µm / Nominal magnification: 73000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |