4S20

Structural basis for transcription reactivation by RapA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.70 Å
  • R-Value Free: 0.369 
  • R-Value Work: 0.273 
  • R-Value Observed: 0.278 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural basis for transcription reactivation by RapA.

Liu, B.Zuo, Y.Steitz, T.A.

(2015) Proc Natl Acad Sci U S A 112: 2006-2010

  • DOI: 10.1073/pnas.1417152112
  • Primary Citation of Related Structures:  
    4S20

  • PubMed Abstract: 
  • RNA polymerase (RNAP) loses activity during transcription as it stalls at various inactive states due to erratic translocation. Reactivation of these stalled RNAPs is essential for efficient RNA synthesis. Here we report a 4.7-Å resolution crystal structure of the Escherichia coli RNAP core enzyme in complex with ATPase RapA that is involved in reactivating stalled RNAPs ...

    RNA polymerase (RNAP) loses activity during transcription as it stalls at various inactive states due to erratic translocation. Reactivation of these stalled RNAPs is essential for efficient RNA synthesis. Here we report a 4.7-Å resolution crystal structure of the Escherichia coli RNAP core enzyme in complex with ATPase RapA that is involved in reactivating stalled RNAPs. The structure reveals that RapA binds at the RNA exit channel of the RNAP and makes the channel unable to accommodate the formation of an RNA hairpin. The orientation of RapA on the RNAP core complex suggests that RapA uses its ATPase activity to propel backward translocation of RNAP along the DNA template in an elongation complex. This structure provides insights into the reactivation of stalled RNA polymerases and helps support ATP-driven backward translocation as a general mechanism for transcriptional regulation.


    Organizational Affiliation

    Department of Molecular Biophysics and Biochemistry, Howard Hughes Medical Institute, and Department of Chemistry, Yale University, New Haven, CT 06520 thomas.steitz@yale.edu.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit alphaA, B, F, G329Escherichia coliMutation(s): 0 
Gene Names: rpoAECDH10B_3470
EC: 2.7.7.6
UniProt
Find proteins for P0A7Z4 (Escherichia coli (strain K12))
Explore P0A7Z4 
Go to UniProtKB:  P0A7Z4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A7Z4
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit betaC, H1,342Escherichia coliMutation(s): 0 
Gene Names: rpoBO3K_23925
EC: 2.7.7.6
UniProt
Find proteins for P0A8V2 (Escherichia coli (strain K12))
Explore P0A8V2 
Go to UniProtKB:  P0A8V2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A8V2
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit beta'D, I1,416Escherichia coliMutation(s): 0 
Gene Names: rpoCO3O_01425
EC: 2.7.7.6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit omegaE, J90Escherichia coliMutation(s): 0 
Gene Names: rpoZO3O_25075
EC: 2.7.7.6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
RNA polymerase-associated protein RapAK, L974Escherichia coliMutation(s): 1 
Gene Names: rapAhepAyabAb0059JW0058
EC: 3.6.4
UniProt
Find proteins for P60240 (Escherichia coli (strain K12))
Explore P60240 
Go to UniProtKB:  P60240
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP60240
Protein Feature View
Expand
  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 6
MoleculeChainsLengthOrganismImage
5'-D(P*AP*CP*GP*AP*CP*TP*GP*AP*GP*CP*CP*GP*AP*TP*G)-3'M, O15N/A
Protein Feature View
Expand
  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 7
MoleculeChainsLengthOrganismImage
5'-R(P*AP*UP*CP*GP*GP*CP*UP*CP*A)-3'N, P9N/A
Protein Feature View
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.70 Å
  • R-Value Free: 0.369 
  • R-Value Work: 0.273 
  • R-Value Observed: 0.278 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 336.09α = 90
b = 158.93β = 101.28
c = 255.01γ = 90
Software Package:
Software NamePurpose
CBASSdata collection
PHASERphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-02-04
    Type: Initial release
  • Version 1.1: 2015-02-18
    Changes: Database references
  • Version 1.2: 2015-03-04
    Changes: Database references