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 

Starting Models: experimental
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This is version 1.3 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: https://doi.org/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. 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.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit alpha
A, B, F, G
329Escherichia coliMutation(s): 0 
Gene Names: rpoAECDH10B_3470
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
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit beta
C, H
1,342Escherichia coliMutation(s): 0 
Gene Names: rpoBO3K_23925
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
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit beta'
D, I
1,416Escherichia coliMutation(s): 0 
Gene Names: rpoCO3O_01425
EC: 2.7.7.6
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit omega
E, J
90Escherichia coliMutation(s): 0 
Gene Names: rpoZO3O_25075
EC: 2.7.7.6
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
RNA polymerase-associated protein RapA
K, L
974Escherichia coliMutation(s): 1 
Gene Names: rapAhepAyabAb0059JW0058
EC: 3.6.4
UniProt
Find proteins for P60240 (Escherichia coli (strain K12))
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UniProt GroupP60240
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  • Reference Sequence

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Entity ID: 6
MoleculeChains LengthOrganismImage
5'-D(P*AP*CP*GP*AP*CP*TP*GP*AP*GP*CP*CP*GP*AP*TP*G)-3'
M, O
15N/A
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Entity ID: 7
MoleculeChains LengthOrganismImage
5'-R(P*AP*UP*CP*GP*GP*CP*UP*CP*A)-3'
N, P
9N/A
Sequence Annotations
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  • 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

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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
  • Version 1.3: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description