3R2D

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.203 

Starting Model: experimental
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This is version 1.6 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: https://doi.org/10.1093/nar/gkr418
  • Primary Citation of Related Structures:  
    3R2C, 3R2D

  • 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, demonstrating that the BoxA RNA is composed of 8 nt 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
N utilization substance protein B
A, B
149Aquifex aeolicusMutation(s): 0 
Gene Names: aq_133nusB
UniProt
Find proteins for O66530 (Aquifex aeolicus (strain VF5))
Explore O66530 
Go to UniProtKB:  O66530
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO66530
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S10C [auth J],
D [auth K]
84Aquifex aeolicusMutation(s): 0 
Gene Names: aq_008NUSErpsJ
UniProt
Find proteins for O66430 (Aquifex aeolicus (strain VF5))
Explore O66430 
Go to UniProtKB:  O66430
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO66430
Sequence Annotations
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  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 3
MoleculeChains LengthOrganismImage
5'-R(*GP*GP*CP*UP*CP*CP*UP*UP*GP*GP*CP*A)-3'E [auth R],
F [auth S]
12Aquifex aeolicus
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.203 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 76.786α = 90
b = 79.94β = 90
c = 106.599γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
SERGUIdata collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-06-22
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2011-10-05
    Changes: Database references
  • Version 1.3: 2017-07-26
    Changes: Advisory, Refinement description, Source and taxonomy
  • Version 1.4: 2017-11-08
    Changes: Refinement description
  • Version 1.5: 2023-08-30
    Changes: Advisory, Data collection, Database references, Derived calculations, Structure summary
  • Version 1.6: 2023-09-13
    Changes: Refinement description