Table S1.
Structural survey of transcription complexes
| NAC conformation | PDB ID | Comments | Reference |
| I TL/open | 1I6H | Yeast Pol II complex with upstream DNA and 13–14 nt RNA synthesized with GTP+ATP+CTP and stalled because of a lack of UTP | (29) |
| 3M3Y | Yeast Pol II complex with pyriplatin-dG:C base pair at initiation + 1 (i+1) site; translocation impaired | (49) | |
| 4Q5S | TthRNAP initiation complex; stressed with σ3.2 blocking of 6-nt RNA | (50) | |
| I → II ? TL/open | 2VUM | Yeast Pol II complex with α-amanitin; translocation intermediate | (31) |
| I ↔ II ? TL/open (failed or incomplete translocation?) | 3RZD | Yeast Pol II complex; hybrid tilted* | (51) |
| 3RZO | Yeast Pol II complex; hybrid tilted* | ||
| 3S1R | Yeast Pol II complex with 3′-deoxy RNA and E site GTP; hybrid tilted* | ||
| 4A3B | Yeast Pol II complex; hybrid tilted* | (52) | |
| 4A3C | Yeast Pol II complex; hybrid tilted* | ||
| 4A3D | Yeast Pol II complex; hybrid tilted* | ||
| 4A3K | Yeast Pol II complex; hybrid tilted* | ||
| 4BY7 | Yeast Pol II complex; hybrid tilted* | (53) | |
| II TL/open | 1SFO | Yeast Pol II complex | (54) |
| 1Y1W | Yeast Pol II complex | (55) | |
| 2JA5 | Yeast Pol II complex | (56) | |
| 2JA6 | Yeast Pol II complex | ||
| 2JA7 | Yeast Pol II complex with dT-dT dimer at i and i+1 sites | ||
| 2JA8 | Yeast Pol II complex with dT-dT dimer at i and i+1 sites; unusual downstream DNA shifts (similar to 4A93) | ||
| 2O5I | TthRNAP complex | (57) | |
| 2R7Z | Yeast Pol II complex with cisplatin-crosslinked T-strand dGi+2 and dGi+3 | (58) | |
| 2R92 | Yeast Pol II complex with RNA stem loop | (59) | |
| 2R93 | Yeast Pol II complex with RNA duplex | ||
| 3H3V | Yeast Pol II complex | (60) | |
| 3HOU | Yeast Pol II complex with dT-U mismatch at i site | (61) | |
| 3HOV | Yeast Pol II complex | ||
| 3HOW | Yeast Pol II complex with dT-U mismatch at i site and frayed 3′-U | ||
| 3HOX | Yeast Pol II complex | ||
| 3HOY | Yeast Pol II complex | ||
| 3HOZ | Yeast Pol II complex with dT-U mismatch at i site, frayed 3′-G | ||
| 3I4M | Yeast Pol II complex with 8-oxo-dG:C base pair at i site, frayed 3′-U | (62) | |
| 3I4N | Yeast Pol II complex with 8-oxo-dG:A base pair at i site, frayed 3′-U | ||
| 3M4O | Yeast Pol II complex with pyriplatin-dG at i+1 site | (49) | |
| 3S14 | Yeast Pol II complex | (51) | |
| 3S15 | Yeast Pol II complex | ||
| 3S16 | Yeast Pol II complex | ||
| 3S17 | Yeast Pol II complex | ||
| 3S1M | Yeast Pol II complex | ||
| 3S1N | Yeast Pol II complex | ||
| 3S2D | Yeast Pol II complex | ||
| 3S2H | Yeast Pol II complex | ||
| 4A3G | Yeast Pol II complex | (52) | |
| 4A93 | Yeast Pol II complex with dT-dT dimer at i+1 and i+2 sites, unusual downstream DNA shifts (similar to 2JA8) | (63) | |
| 4BBS | Yeast Pol II initiation complex with TFIIB | (64) | |
| 4G7O | TthRNAP initiation complex | (18) | |
| 4S20 | EcoRNAP complex with RapA | (47) | |
| 4XLN | TaqRNAP initiation complex with a 13-nt bubble | (17) | |
| 4XLR | TaqRNAP initiation complex with a 13-nt bubble and TthCarD | (65) | |
| 5C3E | Yeast Pol II complex with a 15-nt bubble (upstream invisible) | (66) | |
| 5C44 | Yeast Pol II complex with a 15-nt bubble (upstream invisible) | ||
| 5C4A | Yeast Pol II complex with a 12-nt bubble (upstream invisible) | ||
| 5C4J | Yeast Pol II complex with a 15-nt bubble | ||
| 5C4X | Yeast Pol II complex with a 15-nt bubble | ||
| III TL/open | 1R9S | Yeast Pol II complex with 3′-deoxy RNA and A site UTP | (37) |
| 1R9T | Yeast Pol II complex with 3′-deoxy RNA and E site noncognitive ATP (template dA) | ||
| 1Y77 | Yeast Pol II complex with pre-A site GMPcPP | (55) | |
| 2E2I | Yeast Pol II complex with 3′-deoxy RNA and A site/E site dGTP | (27) | |
| 2E2J | Yeast Pol II complex with A site GMPcPP | ||
| 2NVQ | Yeast Pol II complex with 3′-deoxy RNA and A site/E site dUTP | ||
| 2NVT | Yeast Pol II complex with A site GMPcPP | ||
| 2NVX | Yeast Pol II complex with 3′-deoxy RNA and A site/E site dUTP | ||
| 2YU9 | Yeast Pol II complex with 3′-deoxy RNA and A site/E site UTP | ||
| 2PPB | TthRNAP complex with A site AMPcPP and streptolydigin | (25) | |
| 4OIO | TthRNAP initiation complex with 2 NTPs (ATP and CMPcPP) | (67) | |
| IV? TH/close† | 4A3E | Yeast Pol II complex with A site AMPcPP | (52) |
| 4A3F | Yeast Pol II complex with A site AMPcPP | ||
| 4A3J | Yeast Pol II complex with A site GMPcPP | ||
| 4A3L | Yeast Pol II complex with A site AMPcPP | ||
| 4A3M | Yeast Pol II complex with A site AMPcPP | ||
| 4BY1 | Yeast Pol II complex with A site AMPcPP | (53) | |
| 4Q4Z | TthRNAP initiation complex with 2 NTPs (ATP and CMPcPP) | (50) | |
| IV TH/close | 2E2H | Yeast Pol II complex with 3′-deoxy RNA and A site GTP | (27) |
| 2NVZ | Yeast Pol II complex with 3′-deoxy RNA and A site UTP | ||
| 2O5J | TthRNAP complex with A site AMPcPP | (25) | |
| 3S1Q | Yeast Pol II complex with 3′-deoxy RNA and A site ATP | (51) | |
| V TH/close | σS-EcoRNAP initiation complex with a 14-nt bubble and Ppi | This work | |
| V → VI TH/close | σS-EcoRNAP initiation complex with a 14-nt bubble | This work | |
| σS-EcoRNAP initiation complex with a 14-nt bubble | |||
| VI TH/close | 4YLN | σ70-EcoRNAP initiation complex with a 14-nt bubble | (5) |
| 4YLO | σ70-EcoRNAP initiation complex with a 14-nt bubble | ||
| 4YLP | σ70-EcoRNAP initiation complex with a 15-nt bubble | ||
| Transcription complexes of other conformations | |||
| Ratcheted TL/blocked‡ | 3AOH | TthRNAP complex with Gfh1; cleft open | (68) |
| 3AOI | TthRNAP complex with Gfh1; cleft open | ||
| Elemental pause TL/blocked‡ | 4GZY | TthRNAP complex; cleft open | (69) |
| 4GZZ | TthRNAP complex; cleft open | ||
| Backtracked TL/blocked§ | 3GTG | Yeast Pol II backtracked complex | (70) |
| 3GTJ | Yeast Pol II backtracked complex | ||
| 3GTK | Yeast Pol II backtracked complex | ||
| 3GTL | Yeast Pol II backtracked complex | ||
| 3GTM | Yeast Pol II backtracked complex with TFIIS | ||
| 3GTO | Yeast Pol II backtracked complex | ||
| 3GTP | Yeast Pol II backtracked complex | ||
| 3GTQ | Yeast Pol II backtracked complex | ||
| 3PO2 | Yeast Pol II backtracked complex; hybrid tilted* | (71) | |
| 3PO3 | Yeast Pol II backtracked complex with TFIIS; hybrid tilted* | ||
All available crystal structures of transcription complexes of cellular RNA polymerases as of September 25, 2015 are categorized in regard to their relative conformations in the nucleotide addition cycle (NAC). NAC conformations: I, pretranslocation state with an unfolded TL and an open active site (TL/open); II, posttranslocation state with TL/open; III, posttranslocation state with a bound NTP and an unfolded TL (TL/open); IV, posttranslocation state with a bound NTP and a active site closed by TH formation (TH/close); V, pretranslocation state immediately after catalysis with a PPi-associated and closed active site (TH/close); VI, pretranslocation state after PPi release with the active site remaining closed by THs (TH/close). AMPcPP, α,β-methyleneadenosine 5′-triphosphate; CMPcPP, α,β-methylenecytosine 5′-triphosphate; Eco, Escherichia coli; GMPcPP, α,β-methyleneguanosine 5′-triphosphate; Pol II, RNA polymerase II; Taq, Thermus aquaticus; Tth, Thermus thermophilus.
“Hybrid tilted” refers to the hybrid conformation in which the RNA nucleotide at register n base pairs with the DNA template nucleotide at register n+1.
These structures display a largely folded N-terminal helix of the TL, and thus the active sites are closed, more like that of complex IV.
Both “ratcheted” and “elemental pause” display a cleft-open conformation with a bent BH that is incompatible with the helical conformation of the TL. This bent BH conformation also might be incompatible with A-site/pre–A-site NTP binding.
Backtracked complexes have backtracked RNA residues that prevent NTP binding and are also incompatible with a folded TL conformation.