3L0O | pdb_00003l0o

Structure of RNA-free Rho transcription termination factor from Thermotoga maritima

• PDB DOI: https://doi.org/10.2210/pdb3L0O/pdb

• Classification: HYDROLASE
• Organism(s): Thermotoga maritima
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2009-12-10 Released: 2010-05-26 
• Deposition Author(s): Canals, A., Uson, I., Coll, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free: 
  0.297 (Depositor), 0.290 (DCC) 
• R-Value Work: 
  0.268 (Depositor), 0.260 (DCC) 
• R-Value Observed: 
  0.269 (Depositor) 

Literature

The Structure of RNA-Free Rho Termination Factor Indicates a Dynamic Mechanism of Transcript Capture

Canals, A., Uson, I., Coll, M.

(2010) J Mol Biology 400: 16-23

• PubMed: 20452362 
• DOI: https://doi.org/10.1016/j.jmb.2010.05.004
• Primary Citation of Related Structures:  
  3L0O


• PubMed Abstract: 
  

  The Rho factor is a ring-shaped ATP-dependent helicase that mediates transcription termination in most prokaryotic cells by disengaging the transcription elongation complex formed by the RNA polymerase, DNA, and the nascent RNA transcript. The crystal structures of key intermediates along the kinetic pathway of RNA binding to Rho unveiled an unprecedented mode of helicase loading and provided a model for the ATP turnover coupled to coordinated strand movement. Here we report the structure of the early RNA-free state of Rho, which had eluded crystallization for many years but now completes the series. The structure allows the characterization of the apo-form Rho from Thermotoga maritima to 2.3 A resolution, reveals an RNA-recruiting site that becomes hidden after occupancy of the adjacent specific primary RNA-binding site, and suggests an enriched model for mRNA capture that is consistent with previous data.

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Organizational Affiliation: 

Institute for Research in Biomedicine, Barcelona Science Park, Baldiri Reixac 10, 08028 Barcelona, Spain. [e-mail]

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 99.53 kDa 
• Atom Count: 6,194 
• Modelled Residue Count: 760 
• Deposited Residue Count: 854 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcription termination factor rho	A, B	427	Thermotoga maritima	Mutation(s): 0  EC: 3.6.1 (PDB Primary Data), 3.6.4 (UniProt)
UniProt
Find proteins for P38527 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)) Explore P38527  Go to UniProtKB:  P38527

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
IUM	C [auth A], D [auth A], E [auth A], K [auth B], L [auth B], M [auth B], N [auth B]	URANYL (VI) ION O2 U IZLHQJIUOZHTLW-UHFFFAOYSA-N
SO4	F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], O [auth B], P [auth B], Q [auth B], R [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
NA	S [auth B], T [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free:  0.297 (Depositor), 0.290 (DCC) 
• R-Value Work:  0.268 (Depositor), 0.260 (DCC) 
• R-Value Observed: 0.269 (Depositor) 

Space Group: P 4₃ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 139	α = 90
b = 139	β = 90
c = 150	γ = 90

Software Package:

Software Name	Purpose
DNA	data collection
SHELXS	phasing
REFMAC	refinement
XDS	data reduction
XDS	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-05-26 
Deposition Author(s): Canals, A., Uson, I., Coll, M.

Revision History  

• Version 1.0: 2010-05-26
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2024-03-20
  Changes: Data collection, Database references, Derived calculations