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	Cooperation between bHLH transcription factors and histones for DNA access.
Journal, issue, pages	Nature, Vol. 619, Issue 7969, Page 385-393, Year 2023
Publish date	Jul 5, 2023
Authors	Alicia K Michael / Lisa Stoos / Priya Crosby / Nikolas Eggers / Xinyu Y Nie / Kristina Makasheva / Martina Minnich / Kelly L Healy / Joscha Weiss / Georg Kempf / Simone Cavadini / Lukas Kater / Jan Seebacher / Luca Vecchia / Deyasini Chakraborty / Luke Isbel / Ralph S Grand / Florian Andersch / Jennifer L Fribourgh / Dirk Schübeler / Johannes Zuber / Andrew C Liu / Peter B Becker / Beat Fierz / Carrie L Partch / Jerome S Menet / Nicolas H Thomä /
PubMed Abstract	The basic helix-loop-helix (bHLH) family of transcription factors recognizes DNA motifs known as E-boxes (CANNTG) and includes 108 members. Here we investigate how chromatinized E-boxes are engaged ...The basic helix-loop-helix (bHLH) family of transcription factors recognizes DNA motifs known as E-boxes (CANNTG) and includes 108 members. Here we investigate how chromatinized E-boxes are engaged by two structurally diverse bHLH proteins: the proto-oncogene MYC-MAX and the circadian transcription factor CLOCK-BMAL1 (refs. ). Both transcription factors bind to E-boxes preferentially near the nucleosomal entry-exit sites. Structural studies with engineered or native nucleosome sequences show that MYC-MAX or CLOCK-BMAL1 triggers the release of DNA from histones to gain access. Atop the H2A-H2B acidic patch, the CLOCK-BMAL1 Per-Arnt-Sim (PAS) dimerization domains engage the histone octamer disc. Binding of tandem E-boxes at endogenous DNA sequences occurs through direct interactions between two CLOCK-BMAL1 protomers and histones and is important for circadian cycling. At internal E-boxes, the MYC-MAX leucine zipper can also interact with histones H2B and H3, and its binding is indirectly enhanced by OCT4 elsewhere on the nucleosome. The nucleosomal E-box position and the type of bHLH dimerization domain jointly determine the histone contact, the affinity and the degree of competition and cooperativity with other nucleosome-bound factors.
External links	Nature / PubMed:37407816 / PubMed Central
Methods	EM (single particle)
Resolution	3.3 - 6.2 Å
Structure data	EMDB-17154: Cryo-EM structure of CLOCK-BMAL1 bound to a nucleosomal E-box at position SHL+5.8 (consensus and constituent map 1) Method: EM (single particle) / Resolution: 3.6 Å 17155 8osj EMDB-17155, PDB-8osj: Cryo-EM structure of CLOCK-BMAL1 bound to a nucleosomal E-box at position SHL-6.2 (DNA conformation 1) Method: EM (single particle) / Resolution: 6.2 Å EMDB-17156: Cryo-EM structure of CLOCK-BMAL1 bound to a nucleosomal E-box at position SHL-6.2 (DNA conformation 2) Method: EM (single particle) / Resolution: 3.8 Å 17157 8osk EMDB-17157, PDB-8osk: Cryo-EM structure of CLOCK-BMAL1 bound to a nucleosomal E-box at position SHL+5.8 (composite map) Method: EM (single particle) / Resolution: 3.6 Å EMDB-17158: Cryo-EM structure of CLOCK-BMAL1 bound to a nucleosomal E-box at position SHL+5.8 (constituent map 2 from additional focus classification on PAS domains) Method: EM (single particle) / Resolution: 4.28 Å EMDB-17159: Cryo-EM map of MYC-MAX-OCT4-LIN28 complex Method: EM (single particle) / Resolution: 3.9 Å 17160 8osl EMDB-17160, PDB-8osl: Cryo-EM structure of CLOCK-BMAL1 bound to the native Por enhancer nucleosome (map 2, additional 3D classification and flexible refinement) Method: EM (single particle) / Resolution: 4.9 Å EMDB-17161: Cryo-EM structure of CLOCK-BMAL1 bound to the native Por enhancer nucleosome (map 1) Method: EM (single particle) / Resolution: 3.8 Å EMDB-17162: MAX-MAX bound to a nucleosome at SHL+5.1 and SHL-6.9. Method: EM (single particle) / Resolution: 6.2 Å 17183 8ots EMDB-17183, PDB-8ots: OCT4 and MYC-MAX co-bound to a nucleosome Method: EM (single particle) / Resolution: 3.3 Å 17184 8ott EMDB-17184, PDB-8ott: MYC-MAX bound to a nucleosome at SHL+5.8 Method: EM (single particle) / Resolution: 3.3 Å
Chemicals	ChemComp-PTD: PENTANEDIAL / Glutaraldehyde
Source	homo sapiens (human) Synthetic construct (others) mus musculus (house mouse) aequorea victoria (jellyfish)
Keywords	GENE REGULATION / E-box / transcription factor / circadian clock / TRANSCRIPTION