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Yorodumi- EMDB-10069: Structure of LEDGF PWWP domain bound H3K36 methylated nucleosome -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-10069 | |||||||||
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Title | Structure of LEDGF PWWP domain bound H3K36 methylated nucleosome | |||||||||
Map data | cryo-EM structure of LEDGF bound H3K36me3 modified nucleosome. | |||||||||
Sample |
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Function / homology | Function and homology information supercoiled DNA binding / Integration of viral DNA into host genomic DNA / Autointegration results in viral DNA circles / 2-LTR circle formation / Formation of WDR5-containing histone-modifying complexes / Vpr-mediated nuclear import of PICs / Integration of provirus / APOBEC3G mediated resistance to HIV-1 infection / mRNA 5'-splice site recognition / heterochromatin ...supercoiled DNA binding / Integration of viral DNA into host genomic DNA / Autointegration results in viral DNA circles / 2-LTR circle formation / Formation of WDR5-containing histone-modifying complexes / Vpr-mediated nuclear import of PICs / Integration of provirus / APOBEC3G mediated resistance to HIV-1 infection / mRNA 5'-splice site recognition / heterochromatin / nuclear periphery / euchromatin / structural constituent of chromatin / nucleosome / nucleosome assembly / response to heat / DNA-binding transcription factor binding / response to oxidative stress / transcription coactivator activity / chromatin remodeling / protein heterodimerization activity / chromatin binding / positive regulation of transcription by RNA polymerase II / DNA binding / RNA binding / nucleoplasm / nucleus / cytosol Similarity search - Function | |||||||||
Biological species | Xenopus laevis (African clawed frog) / Homo sapiens (human) / synthetic construct (others) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.2 Å | |||||||||
Authors | Wang H / Farnung L / Dienemann C / Cramer P | |||||||||
Funding support | Germany, 2 items
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Citation | Journal: Nat Struct Mol Biol / Year: 2020 Title: Structure of H3K36-methylated nucleosome-PWWP complex reveals multivalent cross-gyre binding. Authors: Haibo Wang / Lucas Farnung / Christian Dienemann / Patrick Cramer / Abstract: Recognition of histone-modified nucleosomes by specific reader domains underlies the regulation of chromatin-associated processes. Whereas structural studies revealed how reader domains bind modified ...Recognition of histone-modified nucleosomes by specific reader domains underlies the regulation of chromatin-associated processes. Whereas structural studies revealed how reader domains bind modified histone peptides, it is unclear how reader domains interact with modified nucleosomes. Here, we report the cryo-electron microscopy structure of the PWWP reader domain of human transcriptional coactivator LEDGF in complex with an H3K36-methylated nucleosome at 3.2-Å resolution. The structure reveals multivalent binding of the reader domain to the methylated histone tail and to both gyres of nucleosomal DNA, explaining the known cooperative interactions. The observed cross-gyre binding may contribute to nucleosome integrity during transcription. The structure also explains how human PWWP domain-containing proteins are recruited to H3K36-methylated regions of the genome for transcription, histone acetylation and methylation, and for DNA methylation and repair. | |||||||||
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_10069.map.gz | 5.7 MB | EMDB map data format | |
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Header (meta data) | emd-10069-v30.xml emd-10069.xml | 27.6 KB 27.6 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_10069_fsc.xml | 9.1 KB | Display | FSC data file |
Images | emd_10069.png | 226.2 KB | ||
Masks | emd_10069_msk_1.map | 64 MB | Mask map | |
Others | emd_10069_half_map_1.map.gz emd_10069_half_map_2.map.gz | 49.7 MB 49.7 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-10069 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-10069 | HTTPS FTP |
-Validation report
Summary document | emd_10069_validation.pdf.gz | 378.5 KB | Display | EMDB validaton report |
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Full document | emd_10069_full_validation.pdf.gz | 377.6 KB | Display | |
Data in XML | emd_10069_validation.xml.gz | 14.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-10069 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-10069 | HTTPS FTP |
-Related structure data
Related structure data | 6s01MC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_10069.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | cryo-EM structure of LEDGF bound H3K36me3 modified nucleosome. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.05 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
File | emd_10069_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: half map 1
File | emd_10069_half_map_1.map | ||||||||||||
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Annotation | half map 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half map 2
File | emd_10069_half_map_2.map | ||||||||||||
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Annotation | half map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : H3K36me3 nucleosome-LEDGF complex
+Supramolecule #1: H3K36me3 nucleosome-LEDGF complex
+Supramolecule #2: Histone proteins
+Supramolecule #3: PC4 and SFRS1-interacting protein
+Supramolecule #4: Wisdom 601 DNA (165-MER)
+Macromolecule #1: Histone H3
+Macromolecule #2: Histone H4
+Macromolecule #3: Histone H2A
+Macromolecule #4: Histone H2B 1.1
+Macromolecule #7: PC4 and SFRS1-interacting protein
+Macromolecule #5: Wisdom 601 DNA (165-MER)
+Macromolecule #6: Wisdom 601 DNA (165-MER)
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.2 mg/mL | ||||||||||||
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Buffer | pH: 7.5 Component:
Details: Solution were made from stock solution | ||||||||||||
Grid | Model: Quantifoil, UltrAuFoil / Material: GOLD / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR | ||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV / Details: blot for 4 seconds before plunging. | ||||||||||||
Details | the complex is purified by gel filtration |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average exposure time: 9.0 sec. / Average electron dose: 43.18 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |