1S77

T7 RNAP product pyrophosphate elongation complex

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.69 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.251 
  • R-Value Observed: 0.251 

wwPDB Validation 3D Report Full Report


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


Literature

The structural mechanism of translocation and helicase activity in T7 RNA polymerase.

Yin, Y.W., Steitz, T.A.

(2004) Cell 116: 393-404

  • DOI: 10.1016/s0092-8674(04)00120-5
  • Structures With Same Primary Citation

  • PubMed Abstract: 

    • RNA polymerase functions like a molecular motor that can convert chemical energy into the work of strand separation and translocation along the DNA during transcription. The structures of phage T7 RNA polymerase in an elongation phase substrate compl ...

    RNA polymerase functions like a molecular motor that can convert chemical energy into the work of strand separation and translocation along the DNA during transcription. The structures of phage T7 RNA polymerase in an elongation phase substrate complex that includes the incoming nucleoside triphosphate and a pretranslocation product complex that includes the product pyrophosphate (PPi) are described here. These structures and the previously determined posttranslocation elongation complex demonstrate that two enzyme conformations exist during a cycle of single nucleotide addition. One orientation of a five-helix subdomain is stabilized by the phosphates of either the incoming NTP or by the product PPi. A second orientation of this subdomain is stable in their absence and is associated with translocation of the heteroduplex product as well as strand separation of the downstream DNA. We propose that the dissociation of the product PPi after nucleotide addition produces the protein conformational change resulting in translocation and strand separation.

    Organizational Affiliation: 

    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA.



Macromolecules

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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymeraseD883Escherichia phage T7Mutation(s): 0 
Gene Names: 1
EC: 2.7.7.6
Find proteins for P00573 (Escherichia phage T7)
Explore P00573 
Go to UniProtKB:  P00573
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(*TP*TP*TP*AP*CP*GP*TP*TP*GP*CP*GP*CP*AP*CP*GP*GP*C)-3')N17N/A
  • Find similar nucleic acids by: Sequence   |   Structure
Entity ID: 3
MoleculeChainsLengthOrganism
RNA (5'-R(*AP*CP*AP*CP*GP*GP*CP*GP*AP*(3DA))-3')R10N/A

Find similar nucleic acids by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
DNA (5'-D(*GP*CP*CP*GP*TP*GP*CP*GP*CP*AP*TP*TP*CP*GP*CP*CP*GP*TP*GP*TP*T)-3')T21N/A
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
POP
Query on POP
Download CCD File 
D
PYROPHOSPHATE 2-
H2 O7 P2
XPPKVPWEQAFLFU-UHFFFAOYSA-L		 Ligand Interaction
MG
Query on MG
Download CCD File 
D, R
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.69 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.251 
  • R-Value Observed: 0.251 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 127.738α = 90
b = 141.843β = 90
c = 142.856γ = 90
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-03-23
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance