1H38

Structure of a T7 RNA polymerase elongation complex at 2.9A resolution

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.236 
  • R-Value Observed: 0.236 

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This is version 1.2 of the entry. See complete history. 


Literature

Structure of a T7 RNA Polymerase Elongation Complex at 2.9 A Resolution

Tahirov, T.H., Temiakov, D., Anikin, M., Patlan, V., Mcallister, W.T., Vassylyev, D.G., Yokoyama, S.

(2002) Nature 420: 43

  • DOI: 10.1038/nature01129
  • Primary Citation of Related Structures:  
    1H38

  • PubMed Abstract: 

    • The single-subunit bacteriophage T7 RNA polymerase carries out the transcription cycle in an identical manner to that of bacterial and eukaryotic multisubunit enzymes. Here we report the crystal structure of a T7 RNA polymerase elongation complex, which shows that incorporation of an 8-base-pair RNA-DNA hybrid into the active site of the enzyme induces a marked rearrangement of the amino-terminal domain ...

    The single-subunit bacteriophage T7 RNA polymerase carries out the transcription cycle in an identical manner to that of bacterial and eukaryotic multisubunit enzymes. Here we report the crystal structure of a T7 RNA polymerase elongation complex, which shows that incorporation of an 8-base-pair RNA-DNA hybrid into the active site of the enzyme induces a marked rearrangement of the amino-terminal domain. This rearrangement involves alternative folding of about 130 residues and a marked reorientation (about 130 degrees rotation) of a stable core subdomain, resulting in a structure that provides elements required for stable transcription elongation. A wide opening on the enzyme surface that is probably an RNA exit pathway is formed, and the RNA-DNA hybrid is completely buried in a newly formed, deep protein cavity. Binding of 10 base pairs of downstream DNA is stabilized mostly by long-distance electrostatic interactions. The structure implies plausible mechanisms for the various phases of the transcription cycle, and reveals important structural similarities with the multisubunit RNA polymerases.

    Organizational Affiliation: 

    High Throughput Factory, RIKEN Harima Institute at SPring-8, 1-1-1 Kouto, Mikazuki-cho, Sayo, Hyogo 679-5148, Japan.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-DIRECTED RNA POLYMERASEA, B, C, D883Escherichia phage T7Mutation(s): 0 
Gene Names: 1
EC: 2.7.7.6
UniProt
Find proteins for P00573 (Escherichia phage T7)
Explore P00573 
Go to UniProtKB:  P00573
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UniProt GroupP00573
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsLengthOrganismImage
5'-D(*GP*GP*GP*AP*AP*TP*CP*GP*AP*CP *AP*TP*CP*GP*CP*CP*GP*C)-3'E, H, K, N 18Escherichia phage T7
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  • Reference Sequence

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Entity ID: 3
MoleculeChainsLengthOrganismImage
5'-R(*AP*AP*CP*UP*GP*CP*GP*GP*CP*GP *AP*U)-3'F, I, L, O 12Escherichia phage T7
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  • Reference Sequence

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Entity ID: 4
MoleculeChainsLengthOrganismImage
5'-D(*GP*TP*CP*GP*AP*TP*TP*CP*CP*CP)-3'G, J, M, P 10Escherichia phage T7
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.236 
  • R-Value Observed: 0.236 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 79.907α = 90.36
b = 84.971β = 92.97
c = 202.003γ = 109.94
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2002-11-20
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance