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PDBsum entry 3iyd

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Top Page protein dna_rna ligands Protein-protein interface(s) links
Transcription/DNA PDB id
3iyd
Jmol
Contents
Protein chains
322 a.a.
235 a.a.
1089 a.a.
1368 a.a.
90 a.a.
479 a.a.
201 a.a.
DNA/RNA
Ligands
CMP ×2

References listed in PDB file
Key reference
Title Three-Dimensional em structure of an intact activator-Dependent transcription initiation complex.
Authors B.P.Hudson, J.Quispe, S.Lara-González, Y.Kim, H.M.Berman, E.Arnold, R.H.Ebright, C.L.Lawson.
Ref. Proc Natl Acad Sci U S A, 2009, 106, 19830-19835. [DOI no: 10.1073/pnas.0908782106]
PubMed id 19903881
Abstract
We present the experimentally determined 3D structure of an intact activator-dependent transcription initiation complex comprising the Escherichia coli catabolite activator protein (CAP), RNA polymerase holoenzyme (RNAP), and a DNA fragment containing positions -78 to +20 of a Class I CAP-dependent promoter with a CAP site at position -61.5 and a premelted transcription bubble. A 20-A electron microscopy reconstruction was obtained by iterative projection-based matching of single particles visualized in carbon-sandwich negative stain and was fitted using atomic coordinate sets for CAP, RNAP, and DNA. The structure defines the organization of a Class I CAP-RNAP-promoter complex and supports previously proposed interactions of CAP with RNAP alpha subunit C-terminal domain (alphaCTD), interactions of alphaCTD with sigma(70) region 4, interactions of CAP and RNAP with promoter DNA, and phased-DNA-bend-dependent partial wrapping of DNA around the complex. The structure also reveals the positions and shapes of species-specific domains within the RNAP beta', beta, and sigma(70) subunits.
Figure 3.
Class I CAP-RNAP-promoter complex EM reconstruction and fitted model: interactions between CAP, αCTD, and σR4 (stereo pair; density contoured at 2.6σ). Coordinates for CAP, αCTD, σR4, and DNA in this region are based on crystal structures of CAP-αCTD-DNA (8) and αCTD-σR4-DNA. CAP activating region 1 (AR1) is shown in yellow; the 287, 265, and 261 determinants of αCTD are shown in green, red, and blue, respectively; and the 596 determinant of σR4 is shown in pink. Ribbon colors are as in Fig. 2. The protomer of αCTD adjacent to CAP has been linked to αNTD^I, but it alternately could have been linked to αNTD^II (alternate linkage position indicated by black sphere at lower right).
Figure 5.
Class I CAP-RNAP-promoter complex EM reconstruction and fitted model: E. coli species-specific RNAP domains. (A) β′ trigger-loop nonconserved domain (β′GNCD) with β′GNCD SBHMa domain in orange; β′GNCD SBMHb domain in yellow; β′ trigger loop in green; β′ jaw in blue (stereo pair). (B) βDR1. (C) βDR2. (D) β residues 1126–1179 (as well as β N-terminal residues 1–9). (E) σ^70NCR with σ^70NCR insert in green and 20-residue negatively charged loop that is disordered in the crystal structure of the σ^70 fragment (32) indicated as a black dashed line. In each panel, insertion starting and ending points are indicated by black spheres, the EM map is contoured at 2.6σ, and other ribbon colors are as in Fig. 2. Stereo pairs for B–E are shown in Figs. S6 and S7.
PROCHECK
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