5JJI

Rho transcription termination factor bound to rU7 and 6 ADP-BeF3 molecules


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.601 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.219 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Molecular mechanisms of substrate-controlled ring dynamics and substepping in a nucleic acid-dependent hexameric motor.

Thomsen, N.D.Lawson, M.R.Witkowsky, L.B.Qu, S.Berger, J.M.

(2016) Proc. Natl. Acad. Sci. U.S.A. 113: E7691-E7700

  • DOI: 10.1073/pnas.1616745113
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Ring-shaped hexameric helicases and translocases support essential DNA-, RNA-, and protein-dependent transactions in all cells and many viruses. How such systems coordinate ATPase activity between multiple subunits to power conformational changes tha ...

    Ring-shaped hexameric helicases and translocases support essential DNA-, RNA-, and protein-dependent transactions in all cells and many viruses. How such systems coordinate ATPase activity between multiple subunits to power conformational changes that drive the engagement and movement of client substrates is a fundamental question. Using the Escherichia coli Rho transcription termination factor as a model system, we have used solution and crystallographic structural methods to delineate the range of conformational changes that accompany distinct substrate and nucleotide cofactor binding events. Small-angle X-ray scattering data show that Rho preferentially adopts an open-ring state in solution and that RNA and ATP are both required to cooperatively promote ring closure. Multiple closed-ring structures with different RNA substrates and nucleotide occupancies capture distinct catalytic intermediates accessed during translocation. Our data reveal how RNA-induced ring closure templates a sequential ATP-hydrolysis mechanism, provide a molecular rationale for how the Rho ATPase domains distinguishes between distinct RNA sequences, and establish structural snapshots of substepping events in a hexameric helicase/translocase.


    Organizational Affiliation

    Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Transcription termination factor Rho
A, B, C, D, E, F
420Escherichia coli O157:H7Mutation(s): 0 
Gene Names: rho
EC: 3.6.4.-
Find proteins for P0AG32 (Escherichia coli O157:H7)
Go to UniProtKB:  P0AG32
Entity ID: 2
MoleculeChainsLengthOrganism
rU12: 5'-R(P*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)- 3'G12synthetic construct
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
MPD
Query on MPD

Download SDF File 
Download CCD File 
B
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-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: 2.601 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.219 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 68.997α = 90.00
b = 198.567β = 104.36
c = 111.448γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
RESOLVEphasing
PHENIXrefinement
HKL-2000data scaling
PDB_EXTRACTdata extraction
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesGM071747
G. Harold and Leila Y. Mathers FoundationUnited States--

Revision History 

  • Version 1.0: 2016-11-16
    Type: Initial release
  • Version 1.1: 2016-12-21
    Type: Structure summary
  • Version 1.2: 2016-12-28
    Type: Database references
  • Version 1.3: 2017-09-13
    Type: Author supporting evidence