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	Structural insights into γH2Ax containing nucleosomes.
Journal, issue, pages	Nucleic Acids Res, Vol. 53, Issue 19, Year 2025
Publish date	Oct 14, 2025
Authors	Rashmi Panigrahi / Ross Edwards / Md Touhidul Islam / Jun Lu / Ayodeji Kulepa / Tae Hwan Kim / J N Mark Glover /
PubMed Abstract	The phosphorylation of the histone variant H2AX on the nucleosome, yielding γH2AX, acts as a 'master control switch', signaling the recruitment of DNA repair factors at DNA double-stranded break ...The phosphorylation of the histone variant H2AX on the nucleosome, yielding γH2AX, acts as a 'master control switch', signaling the recruitment of DNA repair factors at DNA double-stranded break sites. This phosphorylation is recognized by BRCA1 carboxy-terminal (BRCT) domains of specific repair proteins. Using cryogenic electron microscopy (cryo-EM), we provide structural insights into diverse mononucleosome architectures and inter-nucleosomal interactions in the presence of H2AX, mimicking nucleosomes during DNA repair. We resolved three distinct stacked structures where the nucleosomal dyad axes and disk planes align parallel. The inter-nucleosomal interactions involve unique contacts mediated by the H4 N-terminal tail, exposed H2B elements, and DNA. Geometric analysis of stacking constraints, including published structures, reveals a tight distribution of rotational parameters around 0o, with the greatest variability in the translational parameter 'slide'. Our studies indicate that phosphorylation-dependent binding of BRCT domains with γH2AX nucleosomes disrupts stacking. However, no clear densities for BRCT proteins were observed, indicative of dynamic interactions. Molecular simulations replicate the stability of BRCT binding to γH2AX but do not indicate stable docked conformations of BRCT to nucleosome. We propose that BRCT recognition of γH2AX nucleosomes could contribute to chromatin decondensation during DNA damage signaling, exposing the nucleosomal acidic patch for repair factor recognition.
External links	Nucleic Acids Res / PubMed:41123210 / PubMed Central
Methods	EM (single particle)
Resolution	2.7 - 4.0 Å
Structure data	48375 9mll EMDB-48375, PDB-9mll: GammaH2AX containing nucleosomes, Parallel stack Method: EM (single particle) / Resolution: 3.7 Å 48376 9mln EMDB-48376, PDB-9mln: GammaH2AX containing nucleosome, Canonical (Class 1) Method: EM (single particle) / Resolution: 3.3 Å 48378 9mlr EMDB-48378, PDB-9mlr: GammaH2AX containing nucleosome, Half-wrapped (Class 2) Method: EM (single particle) / Resolution: 3.1 Å 48379 9mls EMDB-48379, PDB-9mls: GammaH2AX containing nucleosome, Extended (Class 3) Method: EM (single particle) / Resolution: 3.6 Å 48392 9mmk EMDB-48392, PDB-9mmk: H2AX containing nucleosome, Canonical (Class 1) Method: EM (single particle) / Resolution: 3.2 Å 48394 9mmm EMDB-48394, PDB-9mmm: H2AX containing nucleosomes, Parallel stack Method: EM (single particle) / Resolution: 4.0 Å 48395 9mmn EMDB-48395, PDB-9mmn: H2AX containing nucleosomes, Left offset stack Method: EM (single particle) / Resolution: 3.6 Å 48396 9mmo EMDB-48396, PDB-9mmo: H2AX containing nucleosomes, Right offset stack Method: EM (single particle) / Resolution: 3.9 Å 48403 9mmt EMDB-48403, PDB-9mmt: H2AX containing nucleosome, Unwrapped (Class 2) Method: EM (single particle) / Resolution: 3.4 Å EMDB-48406: Gamma-H2AX containing nucleosome bound to MCPH1 BRCT Method: EM (single particle) / Resolution: 4.0 Å EMDB-48547: gamma-H2AX containing nucleosome bound to MDC1 BRCT Method: EM (single particle) / Resolution: 2.7 Å
Source	homo sapiens (human) synthetic construct (others)
Keywords	NUCLEAR PROTEIN / phosphorylation / nucleosome / nucleosome stacking