3ICE

Rho transcription termination factor bound to RNA and ADP-BeF3


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.295 
  • R-Value Work: 0.270 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Running in reverse: the structural basis for translocation polarity in hexameric helicases.

Thomsen, N.D.Berger, J.M.

(2009) Cell 139: 523-534

  • DOI: 10.1016/j.cell.2009.08.043

  • PubMed Abstract: 
  • Hexameric helicases couple ATP hydrolysis to processive separation of nucleic acid duplexes, a process critical for gene expression, DNA replication, and repair. All hexameric helicases fall into two families with opposing translocation polarities: t ...

    Hexameric helicases couple ATP hydrolysis to processive separation of nucleic acid duplexes, a process critical for gene expression, DNA replication, and repair. All hexameric helicases fall into two families with opposing translocation polarities: the 3'-->5' AAA+ and 5'-->3' RecA-like enzymes. To understand how a RecA-like hexameric helicase engages and translocates along substrate, we determined the structure of the E. coli Rho transcription termination factor bound to RNA and nucleotide. Interior nucleic acid-binding elements spiral around six bases of RNA in a manner unexpectedly reminiscent of an AAA+ helicase, the papillomavirus E1 protein. Four distinct ATP-binding states, representing potential catalytic intermediates, are coupled to RNA positioning through a complex allosteric network. Comparative studies with E1 suggest that RecA and AAA+ hexameric helicases use different portions of their chemomechanical cycle for translocating nucleic acid and track in opposite directions by reversing the firing order of ATPase sites around the hexameric ring. For a video summary of this article, see the PaperFlick file with the Supplemental Data available online.


    Organizational Affiliation

    Department of Molecular and Cell Biology, Quantitative Biosciences Institute, University of California, Berkeley, CA 94720, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Transcription termination factor rho
A, B, C, D, E, F
422Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rho (nitA, psuA, rnsC, sbaA, tsu)
EC: 3.6.4.-
Find proteins for P0AG30 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AG30
Entity ID: 2
MoleculeChainsLengthOrganism
5'-R(P*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3'G12N/A
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP

Download SDF File 
Download CCD File 
A, B, C, D, E, F
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A, B, C, D, E, F
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
BEF
Query on BEF

Download SDF File 
Download CCD File 
A, B, C, D, E, F
BERYLLIUM TRIFLUORIDE ION
Be F3
OGIAHMCCNXDTIE-UHFFFAOYSA-K
 Ligand Interaction
SPD
Query on SPD

Download SDF File 
Download CCD File 
E, G
SPERMIDINE
N-(2-AMINO-PROPYL)-1,4-DIAMINOBUTANE; PA(34)
C7 H19 N3
ATHGHQPFGPMSJY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B, C, D, E, F
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.295 
  • R-Value Work: 0.270 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 69.230α = 60.48
b = 127.030β = 90.26
c = 127.170γ = 89.77
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
PHASERphasing
HKL-2000data reduction
DENZOdata reduction
SCALEPACKdata scaling
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-11-10
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2012-03-21
    Type: Database references, Refinement description
  • Version 1.3: 2017-11-01
    Type: Refinement description