3IYD

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

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 19.8 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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This is version 1.3 of the entry. See complete history. 


Literature

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

Hudson, B.P., Quispe, J., Lara-Gonzalez, S., Kim, Y., Berman, H.M., Arnold, E., Ebright, R.H., Lawson, C.L.

(2009) Proc Natl Acad Sci U S A 106: 19830-19835

  • DOI: 10.1073/pnas.0908782106
  • Primary Citation of Related Structures:  
    3IYD

  • PubMed 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 ...

    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.

    Organizational Affiliation: 

    Department of Chemistry and Chemical Biology, Rutgers University, 610 Taylor Road, Piscataway, NJ 08854, USA.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit alphaA, B329Escherichia coli K-12Mutation(s): 0 
Gene Names: b3295, JW3257, pez, phs, rpoA, RpoB, RpoC, RpoD, RpoZ, sez
EC: 2.7.7.6
UniProt
Find proteins for P0A7Z4 (Escherichia coli (strain K12))
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UniProt GroupP0A7Z4
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit betaC1,342Escherichia coli K-12Mutation(s): 0 
Gene Names: rpoB, groN, nitB, rif, ron, stl, stv, tabD, b3987, JW3950
EC: 2.7.7.6
UniProt
Find proteins for P0A8V2 (Escherichia coli (strain K12))
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UniProt GroupP0A8V2
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit betaD1,413N/AMutation(s): 0 
EC: 2.7.7.6
UniProt
Find proteins for P0A8T7 (Escherichia coli (strain K12))
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UniProt GroupP0A8T7
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit omegaE90Escherichia coli K-12Mutation(s): 0 
Gene Names: rpoZ, b3649, JW3624
EC: 2.7.7.6
UniProt
Find proteins for P0A800 (Escherichia coli (strain K12))
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
RNA polymerase sigma factor rpoDF613Escherichia coli K-12Mutation(s): 0 
Gene Names: rpoD, alt, b3067, JW3039
UniProt
Find proteins for P00579 (Escherichia coli (strain K12))
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Catabolite gene activatorG, H209Escherichia coli K-12Mutation(s): 0 
Gene Names: crp, cap, csm, b3357, JW5702
UniProt
Find proteins for P0ACJ8 (Escherichia coli (strain K12))
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Entity ID: 7
MoleculeChainsLengthOrganismImage
DNA (98-MER)I98N/A
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Entity ID: 8
MoleculeChainsLengthOrganismImage
DNA (98-MER)J98N/A
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Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CMP
Query on CMP
Download Ideal Coordinates CCD File 
K [auth G],
L [auth H]		ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE
C10 H12 N5 O6 P
IVOMOUWHDPKRLL-KQYNXXCUSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 19.8 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONEMAN
RECONSTRUCTIONSPIDER

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-11-10
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Source and taxonomy, Version format compliance
  • Version 1.2: 2016-02-10
    Changes: Structure summary
  • Version 1.3: 2018-07-18
    Changes: Data collection