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	Subunit specialization in AAA+ proteins and substrate unfolding during transcription complex remodeling.
Journal, issue, pages	Proc Natl Acad Sci U S A, Vol. 122, Issue 17, Page e2425868122, Year 2025
Publish date	Apr 29, 2025
Authors	Forson Gao / Fuzhou Ye / Martin Buck / Xiaodong Zhang /
PubMed Abstract	Bacterial RNA polymerase (RNAP) is a multisubunit enzyme that copies DNA into RNA in a process known as transcription. Bacteria use σ factors to recruit RNAP to promoter regions of genes that need ...Bacterial RNA polymerase (RNAP) is a multisubunit enzyme that copies DNA into RNA in a process known as transcription. Bacteria use σ factors to recruit RNAP to promoter regions of genes that need to be transcribed, with 60% bacteria containing at least one specialized σ factor, σ. σ recruits RNAP to promoters of genes associated with stress responses and forms a stable closed complex that does not spontaneously isomerize to the open state where promoter DNA is melted out and competent for transcription. The σ-mediated open complex formation requires specific AAA+ proteins (TPases ssociated with diverse cellular ctivities) known as bacterial enhancer-binding proteins (bEBPs). We have now obtained structures of new intermediate states of bEBP-bound complexes during transcription initiation, which elucidate the mechanism of DNA melting driven by ATPase activity of bEBPs and suggest a mechanistic model that couples the Adenosine triphosphate (ATP) hydrolysis cycle within the bEBP hexamer with σ unfolding. Our data reveal that bEBP forms a nonplanar hexamer with the hydrolysis-ready subunit located at the furthest/highest point of the spiral hexamer relative to the RNAP. ATP hydrolysis induces conformational changes in bEBP that drives a vectoral transiting of the regulatory N terminus of σ into the bEBP hexamer central pore causing the partial unfolding of σ, while forming specific bEBP contacts with promoter DNA. Furthermore, our data suggest a mechanism of the bEBP AAA+ protein that is distinct from the hand-over-hand mechanism proposed for many other AAA+ proteins, highlighting the versatile mechanisms utilized by the large protein family.
External links	Proc Natl Acad Sci U S A / PubMed:40273105
Methods	EM (single particle)
Resolution	3.9 - 9.4 Å
Structure data	52914 9q91 EMDB-52914, PDB-9q91: CryoEM structure of bacterial transcription intermediate complex mediated by activator PspF containing nifH promoter DNA containing mismatch from -11 to -8 - conformation 6 Method: EM (single particle) / Resolution: 7.2 Å 52916 9q93 EMDB-52916, PDB-9q93: CryoEM structure of bacterial transcription intermediate complex mediated by activator PspF containing nifH promoter DNA containing mismatch from -11 to -8 - conformation 4 Method: EM (single particle) / Resolution: 6.6 Å 52917 9q94 EMDB-52917, PDB-9q94: CryoEM structure of bacterial transcription intermediate complex mediated by activator PspF containing nifH promoter DNA containing mismatch from -11 to -8 - conformation 3 Method: EM (single particle) / Resolution: 5.8 Å 52918 9q95 EMDB-52918, PDB-9q95: CryoEM structure of bacterial transcription intermediate complex mediated by activator PspF containing nifH promoter DNA containing mismatch from -10 to -1 Method: EM (single particle) / Resolution: 6.8 Å 52919 9q96 EMDB-52919, PDB-9q96: Cryo-EM Structure of Bacterial RNA polymerase-sigma54 transcription open complex with wild type sigma54, from RPi(-10-1) Method: EM (single particle) / Resolution: 4.6 Å EMDB-52922: PspF(1-275) subtracted focussed map of bacterial transcription intermediate complex mediated by activator PspF containing nifH promoter DNA containing mismatch from -10 to -1 Method: EM (single particle) / Resolution: 4.7 Å EMDB-52923: PspF(1-275)-DNA-sigma54(R1) focussed map of bacterial transcription intermediate complex mediated by activator PspF containing nifH promoter DNA containing mismatch from -10 to -1 - open clamp conformation Method: EM (single particle) / Resolution: 9.4 Å EMDB-52924: Consensus map of bacterial transcription intermediate complex mediated by activator PspF containing nifH promoter DNA containing mismatch from -10 to -1 - Open clamp conformation Method: EM (single particle) / Resolution: 5.3 Å EMDB-52925: PspF(1-275)-DNA-sigma54(R1) focussed map of bacterial transcription intermediate complex mediated by activator PspF containing nifH promoter DNA containing mismatch from -10 to -1 - Closed clamp conformation Method: EM (single particle) / Resolution: 6.2 Å EMDB-52926: RNA polymerase-sigma54-DNA focussed map of bacterial transcription intermediate complex mediated by activator PspF containing nifH promoter DNA containing mismatch from -10 to -1 - Closed clamp conformation Method: EM (single particle) / Resolution: 5.6 Å EMDB-52927: Consensus map of bacterial transcription intermediate complex mediated by activator PspF containing nifH promoter DNA containing mismatch from -10 to -1 - Closed clamp conformation Method: EM (single particle) / Resolution: 6.8 Å EMDB-52928: RNA polymerase-sigma54-DNA subtracted focussed map of bacterial transcription intermediate complex mediated by activator PspF containing nifH promoter DNA containing mismatch from -11 to -8 - open clamp Method: EM (single particle) / Resolution: 4.2 Å EMDB-52929: RNA polymerase-sigma54-DNA subtracted focussed map of bacterial transcription intermediate complex mediated by activator PspF containing nifH promoter DNA containing mismatch from -11 to -8 - closed clamp Method: EM (single particle) / Resolution: 3.9 Å EMDB-52930: PspF(1-275) subtracted focussed map of bacterial transcription intermediate complex mediated by activator PspF containing nifH promoter DNA containing mismatch from -11 to -8 Method: EM (single particle) / Resolution: 4.7 Å EMDB-52931: PspF(1-275)-DNA-sigma54(R1) focussed map of bacterial transcription intermediate complex mediated by activator PspF containing nifH promoter DNA containing mismatch from -11 to -8 - conformation 6 Method: EM (single particle) / Resolution: 7.07 Å EMDB-52932: RNA polymerase-sigma54-DNA focussed map of bacterial transcription intermediate complex mediated by activator PspF containing nifH promoter DNA containing mismatch from -11 to -8 - conformation 6 Method: EM (single particle) / Resolution: 6.8 Å EMDB-52933: Consensus map of bacterial transcription intermediate complex mediated by activator PspF containing nifH promoter DNA containing mismatch from -11 to -8 - conformation 6 Method: EM (single particle) / Resolution: 7.2 Å EMDB-52934: PspF(1-275)-DNA-sigma54(R1) focussed map of bacterial transcription intermediate complex mediated by activator PspF containing nifH promoter DNA containing mismatch from -11 to -8 - conformation 5 Method: EM (single particle) / Resolution: 6.1 Å EMDB-52935: RNA polymerase-sigma54-DNA focussed map of bacterial transcription intermediate complex mediated by activator PspF containing nifH promoter DNA containing mismatch from -11 to -8 - conformation 5 Method: EM (single particle) / Resolution: 5.9 Å EMDB-52936: Consensus map of bacterial transcription intermediate complex mediated by activator PspF containing nifH promoter DNA containing mismatch from -11 to -8 - conformation 5 Method: EM (single particle) / Resolution: 6.8 Å EMDB-52937: PspF(1-275)-DNA-sigma54(R1) focussed map of bacterial transcription intermediate complex mediated by activator PspF containing nifH promoter DNA containing mismatch from -11 to -8 - conformation 1 Method: EM (single particle) / Resolution: 7.6 Å EMDB-52938: PspF(1-275)-DNA-sigma54(R1) focussed map of bacterial transcription intermediate complex mediated by activator PspF containing nifH promoter DNA containing mismatch from -11 to -8 - conformation 4 Method: EM (single particle) / Resolution: 7.1 Å EMDB-52939: RNA polymerase-sigma54-DNA focussed map of bacterial transcription intermediate complex mediated by activator PspF containing nifH promoter DNA containing mismatch from -11 to -8 - conformation 4 Method: EM (single particle) / Resolution: 6.3 Å EMDB-52940: Consensus map of bacterial transcription intermediate complex mediated by activator PspF containing nifH promoter DNA containing mismatch from -11 to -8 - conformation 4 Method: EM (single particle) / Resolution: 6.6 Å EMDB-52941: Consensus map of bacterial transcription intermediate complex mediated by activator PspF containing nifH promoter DNA containing mismatch from -11 to -8 - conformation 3 Method: EM (single particle) / Resolution: 5.8 Å EMDB-52942: RNA polymerase-sigma54-DNA focussed map of bacterial transcription intermediate complex mediated by activator PspF containing nifH promoter DNA containing mismatch from -11 to -8 - conformation 3 Method: EM (single particle) / Resolution: 5.3 Å EMDB-52943: PspF(1-275)-DNA-sigma54(R1) focussed map of bacterial transcription intermediate complex mediated by activator PspF containing nifH promoter DNA containing mismatch from -11 to -8 - conformation 3 Method: EM (single particle) / Resolution: 5.7 Å EMDB-52944: RNA polymerase-sigma54(R1)-DNA focussed map of bacterial transcription intermediate complex mediated by activator PspF containing nifH promoter DNA containing mismatch from -11 to -8 - conformation 2 Method: EM (single particle) / Resolution: 4.5 Å EMDB-52945: Consensus map of bacterial transcription intermediate complex mediated by activator PspF containing nifH promoter DNA containing mismatch from -11 to -8 - conformation 2 Method: EM (single particle) / Resolution: 4.6 Å EMDB-52946: PspF(1-275)-DNA-sigma54(R1) focussed map of bacterial transcription intermediate complex mediated by activator PspF containing nifH promoter DNA containing mismatch from -11 to -8 - conformation 2 Method: EM (single particle) / Resolution: 6.6 Å 52947 9q97 EMDB-52947, PDB-9q97: CryoEM structure of bacterial transcription intermediate complex mediated by activator PspF containing nifH promoter DNA containing mismatch from -11 to -8 - conformation 2 Method: EM (single particle) / Resolution: 4.6 Å EMDB-52948: RNA polymerase-sigma54-DNA focussed map of bacterial transcription intermediate complex mediated by activator PspF containing nifH promoter DNA containing mismatch from -11 to -8 - conformation 1 Method: EM (single particle) / Resolution: 6.8 Å EMDB-52949: Consensus map of bacterial transcription intermediate complex mediated by activator PspF containing nifH promoter DNA containing mismatch from -11 to -8 - conformation 1 Method: EM (single particle) / Resolution: 6.8 Å 52950 9q98 EMDB-52950: Composite map of bacterial transcription intermediate complex mediated by activator PspF containing nifH promoter DNA containing mismatch from -11 to -8 - conformation 1 PDB-9q98: CryoEM structure of bacterial transcription intermediate complex mediated by activator PspF containing nifH promoter DNA containing mismatch from -11 to -8 - conformation 1 Method: EM (single particle) / Resolution: 8.3 Å
Chemicals	ChemComp-ADP: ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying moleculeYM ChemComp-AF3: ALUMINUM FLUORIDE ChemComp-MG*: Unknown entry
Source	escherichia coli k-12 (bacteria) klebsiella pneumoniae (bacteria)
Keywords	TRANSCRIPTION / sigma factor / complex / AAA+ / DNA-binding protein / TRANSCRIPTION INITIATION / DNA OPENING / TRANSCRIPTION BUBBLE