Three-dimensional animation of the complete bacterial transcription cycle. Press D for a text description of every step, or question mark for keyboard shortcuts.
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5′ 3′ coding 3′ 5′ template 5′ 3′ RNA
Chapter
Structure-informed animation Chemistry at 1× Model & sources ↗
DNA Transcript
Transcript 0 nt
5′ 3′ 0 5 10 15 20 nt clearance ≈10–12 nt
RNA is extended at the end inside RNAP.
01 RNA polymerase
Assembling the core enzyme.
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End of the cycle
The core enzyme is free again. Put these stages in order Drag, or use the arrows
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Find σ70 Template DNA · read 3′→5′ Template Coding DNA Coding RNA · made 5′→3′ RNA
Termination Rho Intrinsic
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× Termination
Follow either ending. The same transcription cycle can end through different molecular mechanisms.
01 / ATP-DEPENDENT MOTOR Rho-dependent Watch Rho load near the older RNA and traverse the long transcript to reach RNAP.
Follow Rho → 02 / RNA STRUCTURE Intrinsic termination Watch a GC-rich RNA hairpin fold beside a U-rich tract and destabilise the complex.
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Where it acts
Read in the notes ↗ × Termination
What was different? Rho-dependent Intrinsic
Protein needed? Yes: the Rho factor No (NusA can assist) Signal in the RNA A rut site upstream of the termination point A GC-rich inverted repeat (hairpin) followed by a U-rich tract Energy ATP, used by Rho’s C-terminal ATPase None beyond RNA folding Helper factor NusG can bridge Rho and RNAP NusA stabilises the hairpin pause Role of pausing A pause gives Rho time to catch up The hairpin and U tract pause and destabilise RNAP Outcome The RNA is released, the DNA rewinds, and the core enzyme can bind σ again How common About half of E. coli terminators are intrinsic (≈1,100 sequences fit the pattern)
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The complete transcription cycle
Preparing molecular structures
× Scientific basis
Structures support RNAP, Rho and NusG use 8E6X and 8E6W . Sigma-70 uses 4YLN , which also supplies the upstream promoter DNA path during initiation (−35 on σ region 4, −10 on σ region 2); NusA uses 6FLQ . Both are aligned through the core enzyme. The α C-terminal domains, which can contact promoter DNA, are not resolved in 8E6X or 4YLN and are not shown (6FLQ resolves them, but only its NusA is used here).
Promoter elements follow 4YLN; the rest of the sequence is an illustrative teaching sequence, with the Rho utilisation site taken from the 8E6W rut RNA. The trigger-loop tip is unresolved in 8E6X, so its folding is schematic. Error-induced backtracking and dinucleotide cleavage follow Zenkin, Yuzenkova & Severinov (2006); in cells GreA and GreB stimulate the cut.
The teaching transcript begins with a short gene (ribosome-binding site AGGAGG, AUG … UAA). With Coupled translation turned on (More, or T), a schematic ribosome (two lobes, not a structure) translates it during the elongation time-lapse while RNAP transcribes, linked by NusG’s KOW domain as in NusG-coupled expressome structures; the rut site lies after the stop codon, in RNA no ribosome covers.
Protein surfaces are smoothed envelopes of deposited coordinates. Protein movement, DNA opening, RNA extension and release are illustrative trajectories, not a molecular-dynamics simulation. The long transcript is a teaching sequence; animation time is slowed and is not elapsed cellular time.
The Rho route represents catch-up along RNA. Exterior RNA contacts and unresolved segments are simplified during the wide view. The intrinsic route shows an RNA hairpin followed by a U-rich tract. Sigma release and RNAP dissociation are shown as common possibilities, not obligatory outcomes in every complex.
Molodtsov et al. · Rho termination · 2023 Zuo & Steitz · Initiation · 2015 You et al. · Intrinsic termination · 2023 Guo et al. · NusA-stabilised pausing · 2018 Zenkin et al. · Transcriptional proofreading · 2006
RNA lengths are displayed in nucleotides. The chip under the header shows how much slower than a cell each stretch plays; cells add about 40–50 nucleotides per second.