Primary Citation PubMed: 23374340
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Published in 2015
The Thermus thermophilus elemental paused elongation complex (ePEC; PDB: 4GZZ) was docked into the RNAP electron density map by superimposing it onto the previously docked homology model of a B. subti... is elongation complex ( 18 ).
Publication Year: 2015
The structure of an elemental-paused elongation complex using Thermus RNAP and DNA/RNA scaffolds derived from the E. coli his-pause sequence showed a unique RNAP conformation including an open-clamp a... d kinked bridge helix that may inhibit processive RNA extension (PDB: 4GZY, 4GZZ) [ 44 ].
Structure PDB code Reference Source Subunit and domain α subunit NTD 1BDF X [ 7 ] A α subunit NTD 4NOI X none F α subunit CTD 1COO N , 3K4G X [ 5 , 8 ] A α subunit CTD 1DOQ N [ 9 ] B α subunit CTD 2MAX N [ 10 ] E β subunit 2/i4 domains 3LTI X [ 11 ] A β subunit flap domain 2LY7 N none C β subunit 1/2 domains 4KBJ X [ 12 ] I β' subunit i2 domain 2AUJ X [ 13 ] B β' subunit i6 domain 2AUK X , 4IQZ X [ 13 ] A σ region 1.1 2K6X N [ 14 ] G, a σ 70 domain2 1SIG X [ 15 ] A, a σ A domains2 and 3 1KU2 X [ 16 ] B, a σ A domain4 1KU3 X [ 16 ] B, a σ A domain4–DNA (−35 element) 1KU7 X [ 16 ] B, a σ A domain4 1TTY N [ 17 ] G, a σ A domain2–DNA (−10 element) 3UGO X , 3UGP X [ 18 ] B, a σ A domain4–αCTD–DNA 3N97 X none B, a, A σ N RpoN–DNA (−24 element) 2O8K N , 2O9L N [ 19 ] D, d σ N core binding domain 2K9M N [ 20 ] D, d σ N RpoN domain 2AHQ N [ 21 ] D, d σ E domain4–DNA (−35 element) 2H27 X [ 22 ] A, c σ C domain2 2O7G X [ 23 ] I, c σ C domain4 2O8X X [ 23 ] I, c σ D domain4 3VFZ X [ 24 ] I, c δ subunit NTD 2KRC N , 4NC7 X , 4NC8 X , 2M4K N , 2KRC N [ 25 , 26 , 27 ] C ε subunit 4NJC X [ 28 ] C RNAP Core enzyme 1HQM X [ 29 , 30 ] B Core enzyme (Δω subunit) 2GHO X [ 31 ] B Holoenzyme 1L9U X , 1IW7 X , 2A6E X , 2CW0 X [ 32 , 33 , 34 ] B Holoenzyme 4YG2 X , 4LJZ X , 4MEY X [ 35 , 36 , 37 ] A Holoenzyme–DNA (−41 ~ −7) 1L9Z X [ 38 ] B Holoenzyme–DNA (−12 ~ +12) 4G7H X , 4G7O X [ 39 ] B de novo initiation complex 4Q4Z X , 4OIO X [ 40 , 41 ] B Initially transcribing complex 4Q5S X [ 40 ] B Elongation complex 2O5I X , 2O5J X [ 42 , 43 ] B Paused elongation complex 4GZY X , 4GZZ X [ 44 ] B Backtracked elongation complex 4WQS X [ 45 ] B A: Escherichia coli ; B: Thermus aquatics/Thermus thermophilus ; C: Bacillus subtilis/Bacilus stearothermophilus ; D: Aquifex aeolicus ; E: Helicobacter pylori ; F: Campylobacter jejuni ; G: Thermotoga maritime ; I: Mycobacterium tuberculosis ; a: group I σ factor; c: extracytoplasmic function (ECF) σ factor; d: σ N /σ 54 factor; X : X-ray crystallography method; N : NMR method.
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