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	Histone H1 binding to nucleosome arrays depends on linker DNA length and trajectory.
Journal, issue, pages	Nat Struct Mol Biol, Vol. 29, Issue 5, Page 493-501, Year 2022
Publish date	May 17, 2022
Authors	Marco Dombrowski / Maik Engeholm / Christian Dienemann / Svetlana Dodonova / Patrick Cramer /
PubMed Abstract	Throughout the genome, nucleosomes often form regular arrays that differ in nucleosome repeat length (NRL), occupancy of linker histone H1 and transcriptional activity. Here, we report cryo-EM ...Throughout the genome, nucleosomes often form regular arrays that differ in nucleosome repeat length (NRL), occupancy of linker histone H1 and transcriptional activity. Here, we report cryo-EM structures of human H1-containing tetranucleosome arrays with four physiologically relevant NRLs. The structures show a zig-zag arrangement of nucleosomes, with nucleosomes 1 and 3 forming a stack. H1 binding to stacked nucleosomes depends on the NRL, whereas H1 always binds to the non-stacked nucleosomes 2 and 4. Short NRLs lead to altered trajectories of linker DNA, and these altered trajectories sterically impair H1 binding to the stacked nucleosomes in our structures. As the NRL increases, linker DNA trajectories relax, enabling H1 contacts and binding. Our results provide an explanation for why arrays with short NRLs are depleted of H1 and suited for transcription, whereas arrays with long NRLs show full H1 occupancy and can form transcriptionally silent heterochromatin regions.
External links	Nat Struct Mol Biol / PubMed:35581345 / PubMed Central
Methods	EM (single particle)
Resolution	3.8 - 11.0 Å
Structure data	13356 7pet EMDB-13356, PDB-7pet: The 4x177 nucleosome array containing H1 Method: EM (single particle) / Resolution: 9.5 Å 13357 7peu EMDB-13357, PDB-7peu: Trinucleosome of the 4x177 nucleosome array containing H1 Method: EM (single particle) / Resolution: 7.2 Å 13358 7pev EMDB-13358, PDB-7pev: Nucleosome stack of the 4x177 nucleosome array containing H1 Method: EM (single particle) / Resolution: 6.0 Å 13359 7pew EMDB-13359, PDB-7pew: Nucleosome 1 of the 4x177 nucleosome array containing H1 Method: EM (single particle) / Resolution: 4.6 Å 13360 7pex EMDB-13360, PDB-7pex: Nucleosome 2 of the 4x177 nucleosome array containing H1 Method: EM (single particle) / Resolution: 5.1 Å 13361 7pey EMDB-13361, PDB-7pey: Nucleosome 3 of the 4x177 nucleosome array containing H1 Method: EM (single particle) / Resolution: 4.5 Å 13362 7pez EMDB-13362, PDB-7pez: Nucleosome 4 of the 4x177 nucleosome array containing H1 Method: EM (single particle) / Resolution: 7.9 Å 13363 7pf0 EMDB-13363, PDB-7pf0: Trinucleosome of the 4x177 nucleosome array containing H1 Method: EM (single particle) / Resolution: 11.0 Å 13365 7pf2 EMDB-13365, PDB-7pf2: Nucleosome stack of the 4x187 nucleosome array containing H1 Method: EM (single particle) / Resolution: 5.1 Å 13366 7pf3 EMDB-13366, PDB-7pf3: Nucleosome 4 of the 4x187 nucleosome array containing H1 Method: EM (single particle) / Resolution: 4.0 Å 13367 7pf4 EMDB-13367, PDB-7pf4: Nucleosome 3 of the 4x187 nucleosome array containing H1 Method: EM (single particle) / Resolution: 4.0 Å 13368 7pf5 EMDB-13368, PDB-7pf5: Nucleosome 2 of the 4x187 nucleosome array containing H1 Method: EM (single particle) / Resolution: 3.8 Å 13369 7pf6 EMDB-13369, PDB-7pf6: Nucleosome 1 of the 4x187 nucleosome array containing H1 Method: EM (single particle) / Resolution: 4.0 Å 13370 7pfa EMDB-13370, PDB-7pfa: Trinucleosome of the 4x197 nucleosome array containing H1 Method: EM (single particle) / Resolution: 9.7 Å 13371 7pfc EMDB-13371, PDB-7pfc: Nucleosome stack of the 4x197 nucleosome array containing H1 Method: EM (single particle) / Resolution: 6.4 Å 13372 7pfd EMDB-13372, PDB-7pfd: Nucleosome 1 of the 4x197 nucleosome array containing H1 Method: EM (single particle) / Resolution: 4.4 Å 13373 7pfe EMDB-13373, PDB-7pfe: Nucleosome 2 of the 4x197 nucleosome array containing H1 Method: EM (single particle) / Resolution: 4.4 Å 13374 7pff EMDB-13374, PDB-7pff: Nucleosome 3 of the 4x197 nucleosome array containing H1 Method: EM (single particle) / Resolution: 4.3 Å 13379 7pft EMDB-13379, PDB-7pft: Trinucleosome of the 4x207 nucleosome array containing H1 Method: EM (single particle) / Resolution: 9.8 Å 13380 7pfu EMDB-13380, PDB-7pfu: Nucleosome stack of the 4x207 nucleosome array containing H1 Method: EM (single particle) / Resolution: 5.0 Å 13381 7pfv EMDB-13381, PDB-7pfv: Nucleosome 1 of the 4x207 nucleosome array containing H1 Method: EM (single particle) / Resolution: 4.4 Å 13382 7pfw EMDB-13382, PDB-7pfw: Nucleosome 2 of the 4x207 nucleosome array containing H1 Method: EM (single particle) / Resolution: 5.2 Å 13383 7pfx EMDB-13383, PDB-7pfx: Nucleosome 3 of the 4x207 nucleosome array containing H1 Method: EM (single particle) / Resolution: 4.3 Å
Source	homo sapiens (human) synthetic construct (others)
Keywords	DNA BINDING PROTEIN / Chromatin / Nucleosomes / Linker Histone / Nucleosome