354D

Structure of loop E FROM E. coli 5S RRNA

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.202 

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This is version 1.4 of the entry. See complete history. 


Literature

Metals, motifs, and recognition in the crystal structure of a 5S rRNA domain.

Correll, C.C., Freeborn, B., Moore, P.B., Steitz, T.A.

(1997) Cell 91: 705-712

  • DOI: https://doi.org/10.1016/s0092-8674(00)80457-2
  • Primary Citation of Related Structures:  
    354D, 357D, 364D

  • PubMed Abstract: 

    Two new RNA structures portray how non-Watson-Crick base pairs and metal ions can produce a unique RNA shape suitable for recognition by proteins. The crystal structures of a 62 nt domain of E. coli 5S ribosomal RNA and a duplex dodecamer encompassing an internal loop E have been determined at 3.0 and 1.5 A, respectively. This loop E region is distorted by three "cross-strand purine stacks" and three novel, water-mediated noncanonical base pairs and stabilized by a four metal ion zipper. These features give its minor groove a unique hydrogen-bonding surface and make the adjacent major groove wide enough to permit recognition by the ribosomal protein L25, which is expected to bind to this surface.

    • Organizational Affiliation: 

    Department of Molecular Biophysics and Biochemistry, Yale University, Howard Hughes Medical Institute, New Haven, Connecticut 06520-8114, USA.


Macromolecules

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Entity ID: 1
MoleculeChains LengthOrganismImage
RNA (5'-R(*CP*CP*GP*AP*UP*GP*GP*UP*AP*GP*UP*G)-3')12Escherichia coli
Sequence Annotations
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  • Reference Sequence

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Entity ID: 2
MoleculeChains LengthOrganismImage
RNA-DNA (5'-R(*GP*CP*GP*AP*GP*AP*GP*UP*AP*)-D(*DGP(S)*)-R(*GP*C)-3')12Escherichia coli
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.202 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.184α = 90
b = 37.654β = 105.9
c = 32.944γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
CNSrefinement
DENZOdata reduction
X-PLORphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1997-11-26
    Type: Initial release
  • Version 1.1: 2008-05-22
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2015-02-18
    Changes: Non-polymer description
  • Version 1.4: 2024-02-21
    Changes: Data collection, Database references, Derived calculations