Structure of LEDGF PWWP domain bound H3K36 methylated nucleosome
Map data
cryo-EM structure of LEDGF bound H3K36me3 modified nucleosome.
Sample
Complex: H3K36me3 nucleosome-LEDGF complex
Complex: Histone proteins
Protein or peptide: Histone H3
Protein or peptide: Histone H4
Protein or peptide: Histone H2A
Protein or peptide: Histone H2B 1.1
Complex: PC4 and SFRS1-interacting protein
Protein or peptide: PC4 and SFRS1-interacting protein
Complex: Wisdom 601 DNA (165-MER)
DNA: Wisdom 601 DNA (165-MER)
DNA: Wisdom 601 DNA (165-MER)
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
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
Deposition
Jun 13, 2019
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Header (metadata) release
Jun 26, 2019
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Map release
Dec 18, 2019
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Update
Jan 22, 2020
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Current status
Jan 22, 2020
Processing site: PDBe / Status: Released
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Structure visualization
Movie
Surface view with section colored by density value
Name: H3K36me3 nucleosome-LEDGF complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#7 Details: H3K36me3 introduced by methyl-lysine analog method, only the density of PWWP domain of LEDGF is visible in the structure
Macromolecule #7: PC4 and SFRS1-interacting protein
Macromolecule
Name: PC4 and SFRS1-interacting protein / type: protein_or_peptide / ID: 7 Details: density of residue 30-34 and residue 92-530 are invisible Number of copies: 1 / Enantiomer: LEVO
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
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Electron microscopy
Microscope
FEI TITAN KRIOS
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
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