3R2D

Crystal Structure of Antitermination Factors NusB and NusE in complex with dsRNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.199 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.201 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Structural basis for RNA recognition by NusB and NusE in the initiation of transcription antitermination.

Stagno, J.R.Altieri, A.S.Bubunenko, M.Tarasov, S.G.Li, J.Court, D.L.Byrd, R.A.Ji, X.

(2011) Nucleic Acids Res. 39: 7803-7815

  • DOI: 10.1093/nar/gkr418
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Processive transcription antitermination requires the assembly of the complete antitermination complex, which is initiated by the formation of the ternary NusB-NusE-BoxA RNA complex. We have elucidated the crystal structure of this complex, demonstra ...

    Processive transcription antitermination requires the assembly of the complete antitermination complex, which is initiated by the formation of the ternary NusB-NusE-BoxA RNA complex. We have elucidated the crystal structure of this complex, demonstrating that the BoxA RNA is composed of 8‚ÄČnt that are recognized by the NusB-NusE heterodimer. Functional biologic and biophysical data support the structural observations and establish the relative significance of key protein-protein and protein-RNA interactions. Further crystallographic investigation of a NusB-NusE-dsRNA complex reveals a heretofore unobserved dsRNA binding site contiguous with the BoxA binding site. We propose that the observed dsRNA represents BoxB RNA, as both single-stranded BoxA and double-stranded BoxB components are present in the classical lambda antitermination site. Combining these data with known interactions amongst antitermination factors suggests a specific model for the assembly of the complete antitermination complex.


    Organizational Affiliation

    Macromolecular Crystallography Laboratory, National Cancer Institute, Frederick, MD 21702, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
N utilization substance protein B
A, B
149Aquifex aeolicus (strain VF5)Mutation(s): 0 
Gene Names: nusB
Find proteins for O66530 (Aquifex aeolicus (strain VF5))
Go to UniProtKB:  O66530
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S10
J, K
84Aquifex aeolicus (strain VF5)Mutation(s): 0 
Gene Names: rpsJ
Find proteins for O66430 (Aquifex aeolicus (strain VF5))
Go to UniProtKB:  O66430
Entity ID: 3
MoleculeChainsLengthOrganism
5'-R(*GP*GP*CP*UP*CP*CP*UP*UP*GP*GP*CP*A)-3'R,S12Aquifex aeolicus
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PEG
Query on PEG

Download SDF File 
Download CCD File 
A, B
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.199 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.201 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 76.786α = 90.00
b = 79.940β = 90.00
c = 106.599γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
PHENIXrefinement
HKL-2000data reduction
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
HKL-2000data scaling
SERGUIdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2011-03-14 
  • Released Date: 2011-06-22 
  • Deposition Author(s): Stagno, J.R., Ji, X.

Revision History 

  • Version 1.0: 2011-06-22
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2011-10-05
    Type: Database references
  • Version 1.3: 2017-07-26
    Type: Advisory, Refinement description, Source and taxonomy
  • Version 1.4: 2017-11-08
    Type: Refinement description