4WQS

Thermus thermophilus RNA polymerase backtracked complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.31 Å
  • R-Value Free: 0.311 
  • R-Value Work: 0.281 
  • R-Value Observed: 0.282 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

The Ratcheted and Ratchetable Structural States of RNA Polymerase Underlie Multiple Transcriptional Functions.

Sekine, S.I.Murayama, Y.Svetlov, V.Nudler, E.Yokoyama, S.

(2015) Mol Cell 57: 408-421

  • DOI: 10.1016/j.molcel.2014.12.014
  • Primary Citation of Related Structures:  
    4WQS, 4WQT

  • PubMed Abstract: 
  • DNA-dependent RNA polymerase (RNAP) accomplishes multiple tasks during transcription by assuming different structural forms. Reportedly, the "tight" form performs nucleotide addition to nascent RNA, while the "ratcheted" form is adopted for transcription inhibition ...

    DNA-dependent RNA polymerase (RNAP) accomplishes multiple tasks during transcription by assuming different structural forms. Reportedly, the "tight" form performs nucleotide addition to nascent RNA, while the "ratcheted" form is adopted for transcription inhibition. In this study, we performed Cys-pair crosslinking (CPX) analyses of various transcription complexes of a bacterial RNAP and crystallographic analyses of its backtracked and Gre-factor-bound states to clarify which of the two forms is adopted. The ratcheted form was revealed to support GreA-dependent transcript cleavage, long backtracking, hairpin-dependent pausing, and termination. In contrast, the tight form correlated with nucleotide addition, mismatch-dependent pausing, one-nucleotide backtracking, and factor-independent transcript cleavage. RNAP in the paused/backtracked state, but not the nucleotide-addition state, readily transitions to the ratcheted form ("ratchetable"), indicating that the tight form represents two distinct regulatory states. The 3' end and the hairpin structure of the nascent RNA promote the ratchetable nature by modulating the trigger-loop conformation.


    Organizational Affiliation

    RIKEN Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan; Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan; RIKEN Structural Biology Laboratory, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan. Electronic address: yokoyama@riken.jp.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit alphaA,
B,
F [auth K],
G [auth L]
315Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpoATTHA1664
EC: 2.7.7.6
UniProt
Find proteins for Q5SHR6 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
Explore Q5SHR6 
Go to UniProtKB:  Q5SHR6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5SHR6
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,
H [auth M]
1119Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpoBTTHA1813
EC: 2.7.7.6
UniProt
Find proteins for Q8RQE9 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
Explore Q8RQE9 
Go to UniProtKB:  Q8RQE9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8RQE9
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,
I [auth N]
1524Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpoCTTHA1812
EC: 2.7.7.6
UniProt
Find proteins for Q8RQE8 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
Explore Q8RQE8 
Go to UniProtKB:  Q8RQE8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8RQE8
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,
J [auth O]
99Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpoZTTHA1561
EC: 2.7.7.6
UniProt
Find proteins for Q8RQE7 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
Explore Q8RQE7 
Go to UniProtKB:  Q8RQE7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8RQE7
Protein Feature View
Expand
  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 5
MoleculeChainsLengthOrganismImage
DNA (28-MER)K [auth G],
N [auth X]
28unidentified
Protein Feature View
Expand
  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 6
MoleculeChainsLengthOrganismImage
RNA (5'-R(P*CP*CP*AP*GP*CP*CP*GP*GP*CP*GP*CP*UP*CP*GP*CP*A)-3')L [auth H],
O [auth Y]
16unidentified
Protein Feature View
Expand
  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 7
MoleculeChainsLengthOrganismImage
DNA (5'-D(P*GP*TP*AP*GP*CP*TP*TP*GP*TP*GP*GP*TP*AP*GP*TP*GP*AP*CP*GP*AP*G)-3')M [auth I],
P [auth Z]
21unidentified
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.31 Å
  • R-Value Free: 0.311 
  • R-Value Work: 0.281 
  • R-Value Observed: 0.282 
  • Space Group: P 41
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 155.983α = 90
b = 155.983β = 90
c = 495γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Cootmodel building
HKL-2000data reduction
HKL-2000data scaling
CNSphasing

Structure Validation

View Full Validation Report




Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of ScienceJapan--

Revision History  (Full details and data files)

  • Version 1.0: 2015-02-18
    Type: Initial release
  • Version 1.1: 2015-09-09
    Changes: Derived calculations
  • Version 1.2: 2015-09-16
    Changes: Other
  • Version 1.3: 2019-12-04
    Changes: Advisory, Data collection, Derived calculations