Biological Assembly 1  

Global Symmetry: Helical - H  (3D View)
Global Stoichiometry: Homo 6-mer - A6 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 288.29 kDa 
• Atom Count: 19,246 
• Modelled Residue Count: 2,407 
• Deposited Residue Count: 2,524 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

 1PVO

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

• PDB DOI:  https://doi.org/10.2210/pdb1PVO/pdb
• NDB: PR0100

• Classification: TRANSCRIPTION/RNA
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2003-06-27 Released: 2003-07-22 
• Deposition Author(s): Skordalakes, E., Berger, J.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 0.304 
• R-Value Work: 0.271 
• R-Value Observed: 0.274 

Literature

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

Skordalakes, E., Berger, J.M.

(2003) Cell 114: 135-146

• PubMed: 12859904 
• DOI: https://doi.org/10.1016/s0092-8674(03)00512-9
• Primary Citation of Related Structures:  
  1PV4, 1PVO


• 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 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcription termination factor rho	F [auth A], G [auth B], H [auth C], I [auth D], J [auth E], K [auth F]	419	Escherichia coli	Mutation(s): 0  Gene Names: rho EC: 3.6.4
UniProt
Find proteins for P0AG30 (Escherichia coli (strain K12)) Explore P0AG30  Go to UniProtKB:  P0AG30

Entity ID: 1
Molecule	Chains	Length	Organism	Image
5'-R(P*UP*C)-3'	A [auth G], B [auth H], C [auth J], D [auth K], E [auth L]	2	N/A

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ANP	L [auth A], M [auth B], N [auth C], O [auth D], P [auth E], Q [auth F]	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER C10 H17 N6 O12 P3 PVKSNHVPLWYQGJ-KQYNXXCUSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 0.304 
• R-Value Work: 0.271 
• R-Value Observed: 0.274 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 119.249	α = 90
b = 204.649	β = 96.54
c = 147.788	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-07-22 
Deposition Author(s): Skordalakes, E., Berger, J.M.

Revision History  

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