Database of articles cited by EMDB/PDB/SASBDB data

Keywords
Structure methods	All X-ray diffraction NMR electron microscopy small angle scattering neutron diffraction fiber diffraction powder diffraction infrared spectroscopy EPR fluorescence transfer theoretical model Hybrid
Author
Journal
IF	>30 >20 >10 >5 all

Title	Multivalency of nucleosome recognition by LEDGF.
Journal, issue, pages	Nucleic Acids Res, Vol. 51, Issue 18, Page 10011-10025, Year 2023
Publish date	Oct 13, 2023
Authors	Eliška Koutná / Vanda Lux / Tomáš Kouba / Jana Škerlová / Jiří Nováček / Pavel Srb / Rozálie Hexnerová / Hana Šváchová / Zdeněk Kukačka / Petr Novák / Milan Fábry / Simon Poepsel / Václav Veverka /
PubMed Abstract	Eukaryotic transcription is dependent on specific histone modifications. Their recognition by chromatin readers triggers complex processes relying on the coordinated association of transcription ...Eukaryotic transcription is dependent on specific histone modifications. Their recognition by chromatin readers triggers complex processes relying on the coordinated association of transcription regulatory factors. Although various modification states of a particular histone residue often lead to differential outcomes, it is not entirely clear how they are discriminated. Moreover, the contribution of intrinsically disordered regions outside of the specialized reader domains to nucleosome binding remains unexplored. Here, we report the structures of a PWWP domain from transcriptional coactivator LEDGF in complex with the H3K36 di- and trimethylated nucleosome, indicating that both methylation marks are recognized by PWWP in a highly conserved manner. We identify a unique secondary interaction site for the PWWP domain at the interface between the acidic patch and nucleosomal DNA that might contribute to an H3K36-methylation independent role of LEDGF. We reveal DNA interacting motifs in the intrinsically disordered region of LEDGF that discriminate between the intra- or extranucleosomal DNA but remain dynamic in the context of dinucleosomes. The interplay between the LEDGF H3K36-methylation reader and protein binding module mediated by multivalent interactions of the intrinsically disordered linker with chromatin might help direct the elongation machinery to the vicinity of RNA polymerase II, thereby facilitating productive elongation.
External links	Nucleic Acids Res / PubMed:37615563 / PubMed Central
Methods	EM (single particle)
Resolution	2.69 - 4.0 Å
Structure data	16546 8cbn EMDB-16546, PDB-8cbn: structure of LEDGF/p75 PWWP domain bound to the H3K36 trimethylated dinucleosome Method: EM (single particle) / Resolution: 3.34 Å 16549 8cbq EMDB-16549, PDB-8cbq: structure of LEDGF/p75 PWWP domain bound to the H3K36 trimethylated dinucleosome Method: EM (single particle) / Resolution: 4.0 Å 17594 8pc5 EMDB-17594, PDB-8pc5: H3K36me3 nucleosome-LEDGF/p75 PWWP domain complex Method: EM (single particle) / Resolution: 3.02 Å 17595 8pc6 EMDB-17595, PDB-8pc6: H3K36me3 nucleosome-LEDGF/p75 PWWP domain complex - pose 2 Method: EM (single particle) / Resolution: 3.04 Å 17633 8peo EMDB-17633, PDB-8peo: H3K36me2 nucleosome-LEDGF/p75 PWWP domain complex Method: EM (single particle) / Resolution: 2.69 Å 17634 8pep EMDB-17634, PDB-8pep: H3K36me2 nucleosome-LEDGF/p75 PWWP domain complex - pose 2 Method: EM (single particle) / Resolution: 3.33 Å
Chemicals	ChemComp-M2L: (2R)-2-amino-3-(2-dimethylaminoethylsulfanyl)propanoic acid
Source	xenopus laevis (African clawed frog) synthetic construct (others) homo sapiens (human)
Keywords	TRANSCRIPTION / nucleosome / transcription activator / methylation / complex / DNA BINDING PROTEIN / transcription elongation