Fig. 3: Pol V does not interact with the initiation and elongation factors of Pol II and Pol IV.
From: A cryo-EM structure of KTF1-bound polymerase V transcription elongation complex
a Pol V is not compatible with RDR2. The upper panel shows clashes between the modeled RDR2 (purple surface; based on superimposition of the Pol IV-RDR2 (PDB: 7EU0) and Pol V TEC structures) and Pol V. The red rectangle indicates clashes between the modeled RDR2 and the zinc ribbon domain of NRP(B/D/E)9. The lower panel shows the interaction between RDR2 and Pol IV in the Pol IV-RDR2 structure (PDB: 7EU0)18. The Pol IV-specific insertion of at the funnel helix tip (NRPD1-FHT) is highlighted by dashes. b Pol V is incompatible with TFIIS binding. The red rectangle indicates clashes between the modeled TFIIS (based on superimposition of the Pol II-TFIIS (PDB: 1Y1V) and Pol V structures)53 and the zinc ribbon domain of NRP(B/D/E)9 shown in cryo-EM map and ribbon. c The surface patches of Pol V is incapable of interaction with TFIIB, d TFIIE, and e TFIIF. TFIIB, TFIIE, and TFIIF are modeled on the Pol V TEC structure based on the superimposition between human Pol II PIC (PDB: 5IYC)54 and Pol V TEC. The red surface patches highlight non-conserved residues of Pol V on the corresponding initiation factors-contact surfaces of Pol II.
