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3iyd

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3iyd, resolution 19.80Å ()
Ligands:
Gene: b3295, JW3257, pez, phs, rpoA, RpoB, RpoC, RpoD, RpoZ, sez (Escherichia coli), rpoB, groN, nitB, rif, ron, stl, stv, tabD, b3987, JW3950 (Escherichia coli), rpoZ, b3649, JW3624 (Escherichia coli K-12), rpoD (Escherichia coli K-12), crp, cap, csm, b3357, JW5702 (Escherichia coli K-12)
Activity: DNA-directed RNA polymerase, with EC number 2.7.7.6
Resources: FirstGlance, OCA, PDBsum, RCSB
Coordinates: save as pdb, mmCIF, xml



Contents

Three-dimensional EM structure of an intact activator-dependent transcription initiation complex

Publication Abstract from PubMed

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.

Three-dimensional EM structure of an intact activator-dependent transcription initiation complex., Hudson BP, Quispe J, Lara-Gonzalez S, Kim Y, Berman HM, Arnold E, Ebright RH, Lawson CL, Proc Natl Acad Sci U S A. 2009 Nov 24;106(47):19830-5. Epub 2009 Nov 10. PMID:19903881

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

About this Structure

3iyd is a 10 chain structure with sequence from Escherichia coli and Escherichia coli k-12. Full crystallographic information is available from OCA.

See Also

Reference

  • Hudson BP, Quispe J, Lara-Gonzalez S, Kim Y, Berman HM, Arnold E, Ebright RH, Lawson CL. Three-dimensional EM structure of an intact activator-dependent transcription initiation complex. Proc Natl Acad Sci U S A. 2009 Nov 24;106(47):19830-5. Epub 2009 Nov 10. PMID:19903881

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