Extended Data Fig. 7: MYC-MAX and OCT4 cooperatively bind to a nucleosome by releasing nucleosomal DNA.
From: Cooperation between bHLH transcription factors and histones for DNA access
a, Map density around MYC-MAX at position SHL+5.1, contoured at 0.0121 (map postprocessed by LocScale). b, A second diffuse MYC-MAX heterodimer is present in some classes (see also Extended Data Fig. 6g) at SHL-6.9. c,d, Comparison of OCT4–MYC-MAX-Widom 601 (c) and the OCT4–MYC-MAX-LIN28-E nucleosome (d) complexes. e, Representative cryo-EM micrograph of 8,603 micrographs, denoised with Janni. f, Processing scheme. The movies were pre-processed with cryoFLARE and the resulting movies were imported in RELION for motion correction, CTF estimation and particle picking. Ab-initio (cryoSPARC) in combination with 3D classification (RELION) resulted in a homogenous subset of particles that were used for the final 3D reconstruction. The boxes defined by dashed line indicate the good models and set of particles used for the following step in the data processing workflow. g, Angular distribution for the particles leading to the 3.8 Å resolution map. h, Local-resolution filtered map (MonoRes) highlighted by red dashed box shown in f. i, Gold-standard FSC curve for the 3.8 Å resolution map highlighted by the red dashed box shown in f. j, Map density around the interface between the basic loop of MYC or MAX and H2B, contoured at 0.13. k, Map density around a contact between MYC or MAX and H2B/H2A, contoured at 0.096. Maps were postprocessed by LocScale88. Residues Tyr73 and Arg76 in MAX were mutated to Ala and residues Ser405 and Ala408 in MYC were mutated to Tyr and Arg, respectively to mimic the residues in MAX, making MYC more MAX-like for smTIRF experiments (see also Extended Data Fig. 8a–n). l, Cross-link between MYC basic loop and H2A lysines (spheres). The cross-linker was DSSO and indicated distances (dashes) are between lysine Cα atoms. m,n, Close-up of the TF–histone interface for both MYC-MAX orientations, highlighting potentially contacting residues between H2A/H2B and the LZ. Side-chain rotamers, shown here, are modelled, as clear density was missing.
