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 visualization of transcription initiation in action.
Journal, issue, pages	Science, Vol. 382, Issue 6677, Page eadi5120, Year 2023
Publish date	Dec 22, 2023
Authors	Xizi Chen / Weida Liu / Qianmin Wang / Xinxin Wang / Yulei Ren / Xuechun Qu / Wanjun Li / Yanhui Xu /
PubMed Abstract	Transcription initiation is a complex process, and its mechanism is incompletely understood. We determined the structures of de novo transcribing complexes TC2 to TC17 with RNA polymerase II halted ...Transcription initiation is a complex process, and its mechanism is incompletely understood. We determined the structures of de novo transcribing complexes TC2 to TC17 with RNA polymerase II halted on G-less promoters when nascent RNAs reach 2 to 17 nucleotides in length, respectively. Connecting these structures generated a movie and a working model. As initially synthesized RNA grows, general transcription factors (GTFs) remain bound to the promoter and the transcription bubble expands. Nucleoside triphosphate (NTP)-driven RNA-DNA translocation and template-strand accumulation in a nearly sealed channel may promote the transition from initially transcribing complexes (ITCs) (TC2 to TC9) to early elongation complexes (EECs) (TC10 to TC17). Our study shows dynamic processes of transcription initiation and reveals why ITCs require GTFs and bubble expansion for initial RNA synthesis, whereas EECs need GTF dissociation from the promoter and bubble collapse for promoter escape.
External links	Science / PubMed:38127763
Methods	EM (single particle)
Resolution	2.72 - 11.47 Å
Structure data	37395 8wak EMDB-37395, PDB-8wak: Structure of transcribing complex 2 (TC2), the initially transcribing complex with Pol II positioned 2nt downstream of TSS. Method: EM (single particle) / Resolution: 5.47 Å 37396 8wal EMDB-37396, PDB-8wal: Structure of transcribing complex 3 (TC3), the initially transcribing complex with Pol II positioned 3nt downstream of TSS. Method: EM (single particle) / Resolution: 8.52 Å 37398 8wan EMDB-37398, PDB-8wan: Structure of transcribing complex 4 (TC4), the initially transcribing complex with Pol II positioned 4nt downstream of TSS. Method: EM (single particle) / Resolution: 6.07 Å 37399 8wao EMDB-37399, PDB-8wao: Structure of transcribing complex 5 (TC5), the initially transcribing complex with Pol II positioned 5nt downstream of TSS. Method: EM (single particle) / Resolution: 6.4 Å 37400 8wap EMDB-37400, PDB-8wap: Structure of transcribing complex 6 (TC6), the initially transcribing complex with Pol II positioned 6nt downstream of TSS. Method: EM (single particle) / Resolution: 5.85 Å 37401 8waq EMDB-37401, PDB-8waq: Structure of transcribing complex 7 (TC7), the initially transcribing complex with Pol II positioned 7nt downstream of TSS. Method: EM (single particle) / Resolution: 6.29 Å 37402 8war EMDB-37402, PDB-8war: Structure of transcribing complex 8 (TC8), the initially transcribing complex with Pol II positioned 8nt downstream of TSS. Method: EM (single particle) / Resolution: 7.2 Å 37403 8was EMDB-37403, PDB-8was: Structure of transcribing complex 9 (TC9), the initially transcribing complex with Pol II positioned 9nt downstream of TSS. Method: EM (single particle) / Resolution: 6.13 Å 37404 8wat EMDB-37404, PDB-8wat: De novo transcribing complex 10 (TC10), the early elongation complex with Pol II positioned 10nt downstream of TSS Method: EM (single particle) / Resolution: 2.82 Å 37405 8wau EMDB-37405, PDB-8wau: De novo transcribing complex 11 (TC11), the early elongation complex with Pol II positioned 11nt downstream of TSS Method: EM (single particle) / Resolution: 2.78 Å 37406 8wav EMDB-37406, PDB-8wav: De novo transcribing complex 12 (TC12), the early elongation complex with Pol II positioned 12nt downstream of TSS Method: EM (single particle) / Resolution: 2.72 Å 37407 8waw EMDB-37407, PDB-8waw: De novo transcribing complex 13 (TC13), the early elongation complex with Pol II positioned 13nt downstream of TSS Method: EM (single particle) / Resolution: 3.02 Å 37408 8wax EMDB-37408, PDB-8wax: De novo transcribing complex 14 (TC14), the early elongation complex with Pol II positioned 14nt downstream of TSS Method: EM (single particle) / Resolution: 2.75 Å 37409 8way EMDB-37409, PDB-8way: De novo transcribing complex 15 (TC15), the early elongation complex with Pol II positioned 15nt downstream of TSS Method: EM (single particle) / Resolution: 2.85 Å 37410 8waz EMDB-37410, PDB-8waz: De novo transcribing complex 16 (TC16), the early elongation complex with Pol II positioned 16nt downstream of TSS Method: EM (single particle) / Resolution: 2.76 Å 37411 8wb0 EMDB-37411, PDB-8wb0: De novo transcribing complex 17 (TC17), the early elongation complex with Pol II positioned 17nt downstream of TSS Method: EM (single particle) / Resolution: 2.94 Å EMDB-37412: De novo transcribing complex 9 (AdML9G), the initially transcribing complex with Pol II positioned 9nt downstream of TSS Method: EM (single particle) / Resolution: 11.47 Å EMDB-37413: De novo transcribing complex 10 (AdML10G), the early elongation complex with Pol II positioned 10nt downstream of TSS. Method: EM (single particle) / Resolution: 3.47 Å
Chemicals	ChemComp-ZN: Unknown entry ChemComp-SF4: IRON/SULFUR CLUSTER / Iron–sulfur cluster ChemComp-W0F: [[(2~{S},3~{R},4~{S},5~{R})-5-(2-azanyl-6-oxidanylidene-3~{H}-purin-9-yl)-3-methoxy-4-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate ChemComp-MG: Unknown entry
Source	homo sapiens (human) sus scrofa (pig) synthetic construct (others) amanita phalloides (death cap)
Keywords	TRANSCRIPTION / transcribing complex / de novo transcription initiation / initially transcribing complex (ITC) / early elongation complex (EEC)