1PVO

X-ray crystal structure of Rho transcription termination factor in complex with ssRNA substrate and ANPPNP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.304 
  • R-Value Work: 0.271 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structure of the Rho transcription terminator: mechanism of mRNA recognition and helicase loading

Skordalakes, E.Berger, J.M.

(2003) Cell 114: 135-146

  • Primary Citation of Related Structures:  1PV4

  • PubMed Abstract: 
  • In bacteria, one of the major transcriptional termination mechanisms requires a RNA/DNA helicase known as the Rho factor. We have determined two structures of Rho complexed with nucleic acid recognition site mimics in both free and nucleotide bound s ...

    In bacteria, one of the major transcriptional termination mechanisms requires a RNA/DNA helicase known as the Rho factor. We have determined two structures of Rho complexed with nucleic acid recognition site mimics in both free and nucleotide bound states to 3.0 A resolution. Both structures show that Rho forms a hexameric ring in which two RNA binding sites--a primary one responsible for target mRNA recognition and a secondary one required for mRNA translocation and unwinding--point toward the center of the ring. Rather than forming a closed ring, the Rho hexamer is split open, resembling a "lock washer" in its global architecture. The distance between subunits at the opening is sufficiently wide (12 A) to accommodate single-stranded RNA. This open configuration most likely resembles a state poised to load onto mRNA and suggests how related ring-shaped enzymes may be breached to bind nucleic acids.


    Organizational Affiliation

    Department of Molecular and Cell Biology, University of California, Berkeley, 239 Hildebrand Hall, #3206, Berkeley, CA 94720, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Transcription termination factor rho
A, B, C, D, E, F
419Escherichia coli (strain K12)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(P*UP*C)-3'G,H,J,K,L2N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ANP
Query on ANP

Download SDF File 
Download CCD File 
A, B, C, D, E, F
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
C10 H17 N6 O12 P3
PVKSNHVPLWYQGJ-KQYNXXCUSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.304 
  • R-Value Work: 0.271 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 119.249α = 90.00
b = 204.649β = 96.54
c = 147.788γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
AMoREphasing
REFMACrefinement
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-07-22
    Type: Initial release
  • Version 1.1: 2008-04-29
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Advisory, Version format compliance
  • Version 1.3: 2018-01-31
    Type: Experimental preparation