2HT1

The closed ring structure of the Rho transcription termination factor in complex with nucleic acid in the motor domains


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.51 Å
  • R-Value Free: 0.328 
  • R-Value Work: 0.294 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural Insights into RNA-Dependent Ring Closure and ATPase Activation by the Rho Termination Factor.

Skordalakes, E.Berger, J.M.

(2006) Cell 127: 553-564

  • DOI: 10.1016/j.cell.2006.08.051

  • PubMed Abstract: 
  • Hexameric helicases and translocases are required for numerous essential nucleic-acid transactions. To better understand the mechanisms by which these enzymes recognize target substrates and use nucleotide hydrolysis to power molecular movement, we h ...

    Hexameric helicases and translocases are required for numerous essential nucleic-acid transactions. To better understand the mechanisms by which these enzymes recognize target substrates and use nucleotide hydrolysis to power molecular movement, we have determined the structure of the Rho transcription termination factor, a hexameric RNA/DNA helicase, with single-stranded RNA bound to the motor domains of the protein. The structure reveals a closed-ring "trimer of dimers" conformation for the hexamer that contains an unanticipated arrangement of conserved loops required for nucleic-acid translocation. RNA extends across a shallow intersubunit channel formed by conserved amino acids required for RNA-stimulated ATP hydrolysis and translocation and directly contacts a conserved lysine, just upstream of the catalytic GKT triad, in the phosphate-binding (P loop) motif of the ATP-binding pocket. The structure explains the molecular effects of numerous mutations and provides new insights into the links between substrate recognition, ATP turnover, and coordinated strand movement.


    Organizational Affiliation

    Department of Molecular and Cell Biology, University of California, Berkeley, 327B Hildebrand Hall #3206, Berkeley, CA 94720, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Transcription termination factor rho
A, B
433Escherichia 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: 1
MoleculeChainsLengthOrganism
5'-R(*UP*C)-3'J,K2N/A
Entity ID: 2
MoleculeChainsLengthOrganism
5'-R(*UP*CP*UP*CP*U)-3'M5N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.51 Å
  • R-Value Free: 0.328 
  • R-Value Work: 0.294 
  • Space Group: I 4 3 2
Unit Cell:
Length (Å)Angle (°)
a = 257.686α = 90.00
b = 257.686β = 90.00
c = 257.686γ = 90.00
Software Package:
Software NamePurpose
CCP4data scaling
MOSFLMdata reduction
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-11-14
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Advisory, Version format compliance