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PDBsum entry 3iyd

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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
* Residue conservation analysis
PDB id:
3iyd
Name: Transcription/DNA
Title: Three-dimensional em structure of an intact activator-depend transcription initiation complex
Structure: DNA-directed RNA polymerase subunit alpha. Chain: a, b. Fragment: rnap polymerase (sigma70 holoenzyme). Synonym: rnap subunit alpha, transcriptase subunit alpha, r polymerase subunit alpha. Engineered: yes. DNA-directed RNA polymerase subunit beta. Chain: c. Fragment: catabolite activator protein.
Source: Escherichia coli. Organism_taxid: 83333. Strain: k-12. Gene: b3295, jw3257, pez, phs, rpoa, rpob, rpoc, rpod, rpoz expressed in: escherichia coli. Expression_system_taxid: 562. Gene: rpob, gron, nitb, rif, ron, stl, stv, tabd, b3987, jw synthetic: yes. Other_details: purchased from idt and annealed.
Authors: B.P.Hudson,J.Quispe,S.Lara,Y.Kim,H.Berman,E.Arnold,R.H.Ebrig C.L.Lawson
Key ref:
B.P.Hudson et al. (2009). Three-dimensional EM structure of an intact activator-dependent transcription initiation complex. Proc Natl Acad Sci U S A, 106, 19830-19835. PubMed id: 19903881 DOI: 10.1073/pnas.0908782106
Date:
01-Aug-09     Release date:   10-Nov-09    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P0A7Z4  (RPOA_ECOLI) -  DNA-directed RNA polymerase subunit alpha
Seq:
Struc:
329 a.a.
322 a.a.
Protein chain
Pfam   ArchSchema ?
P0A7Z4  (RPOA_ECOLI) -  DNA-directed RNA polymerase subunit alpha
Seq:
Struc:
329 a.a.
235 a.a.
Protein chain
Pfam   ArchSchema ?
P0A8V2  (RPOB_ECOLI) -  DNA-directed RNA polymerase subunit beta
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
1342 a.a.
1089 a.a.
Protein chain
Pfam   ArchSchema ?
P0A8T7  (RPOC_ECOLI) -  DNA-directed RNA polymerase subunit beta'
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
1407 a.a.
1368 a.a.
Protein chain
Pfam   ArchSchema ?
P0A800  (RPOZ_ECOLI) -  DNA-directed RNA polymerase subunit omega
Seq:
Struc:
91 a.a.
90 a.a.
Protein chain
Pfam   ArchSchema ?
P00579  (RPOD_ECOLI) -  RNA polymerase sigma factor RpoD
Seq:
Struc:
 
Seq:
Struc:
613 a.a.
479 a.a.*
Protein chains
Pfam   ArchSchema ?
P0ACJ8  (CRP_ECOLI) -  cAMP-activated global transcriptional regulator CRP
Seq:
Struc:
210 a.a.
201 a.a.
Key:    PfamA domain  Secondary structure
* PDB and UniProt seqs differ at 3 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: Chains A, B, C, D, E: E.C.2.7.7.6  - DNA-directed Rna polymerase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1)
Nucleoside triphosphate
+ RNA(n)
= diphosphate
+ RNA(n+1)
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     membrane   5 terms 
  Biological process     transcription initiation from bacterial-type RNA polymerase promoter   10 terms 
  Biochemical function     protein binding     12 terms  

 

 
    reference    
 
 
DOI no: 10.1073/pnas.0908782106 Proc Natl Acad Sci U S A 106:19830-19835 (2009)
PubMed id: 19903881  
 
 
Three-dimensional EM structure of an intact activator-dependent transcription initiation complex.
B.P.Hudson, J.Quispe, S.Lara-González, Y.Kim, H.M.Berman, E.Arnold, R.H.Ebright, C.L.Lawson.
 
  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.
 
  Selected figure(s)  
 
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.
 
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
  20856905 N.Opalka, J.Brown, W.J.Lane, K.A.Twist, R.Landick, F.J.Asturias, and S.A.Darst (2010).
Complete structural model of Escherichia coli RNA polymerase from a hybrid approach.
  PLoS Biol, 8, 0.
PDB codes: 3lti 3lu0
20606261 S.Lara-González, J.J.Birktoft, and C.L.Lawson (2010).
Structure of the Escherichia coli RNA polymerase alpha subunit C-terminal domain.
  Acta Crystallogr D Biol Crystallogr, 66, 806-812.
PDB code: 3k4g
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.