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PDBsum entry 5c4x
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Transferase/RNA/DNA
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PDB id
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5c4x
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Contents |
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1436 a.a.
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1172 a.a.
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265 a.a.
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178 a.a.
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214 a.a.
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87 a.a.
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171 a.a.
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135 a.a.
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114 a.a.
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66 a.a.
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115 a.a.
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44 a.a.
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References listed in PDB file
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Key reference
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Title
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Crystal structure of a transcribing RNA polymerase ii complex reveals a complete transcription bubble.
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Authors
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C.O.Barnes,
M.Calero,
I.Malik,
B.W.Graham,
H.Spahr,
G.Lin,
A.E.Cohen,
I.S.Brown,
Q.Zhang,
F.Pullara,
M.A.Trakselis,
C.D.Kaplan,
G.Calero.
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Ref.
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Mol Cell, 2015,
59,
258-269.
[DOI no: ]
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PubMed id
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Abstract
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Notwithstanding numerous published structures of RNA Polymerase II (Pol II),
structural details of Pol II engaging a complete nucleic acid scaffold have been
lacking. Here, we report the structures of TFIIF-stabilized transcribing Pol II
complexes, revealing the upstream duplex and full transcription bubble. The
upstream duplex lies over a wedge-shaped loop from Rpb2 that engages its minor
groove, providing part of the structural framework for DNA tracking during
elongation. At the upstream transcription bubble fork, rudder and fork loop 1
residues spatially coordinate strand annealing and the nascent RNA transcript.
At the downstream fork, a network of Pol II interactions with the non-template
strand forms a rigid domain with the trigger loop (TL), allowing visualization
of its open state. Overall, our observations suggest that
"open/closed" conformational transitions of the TL may be linked to
interactions with the non-template strand, possibly in a synchronized ratcheting
manner conducive to polymerase translocation.
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