1LNT

Crystal Structure of the Highly Conserved RNA Internal Loop of SRP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.200 

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This is version 1.3 of the entry. See complete history


Literature

Structure of an RNA dodecamer containing a fragment from SRP domain IV of Escherichia coli.

Deng, J.Xiong, Y.Pan, B.Sundaralingam, M.

(2003) Acta Crystallogr D Biol Crystallogr 59: 1004-1011

  • DOI: 10.1107/s0907444903006747
  • Primary Citation of Related Structures:  
    1LNT

  • PubMed Abstract: 
  • The crystal structure of an RNA dodecamer, r(GCGUCAGGUC(Br)CG)/r(CGGAAGCAG(Br)CGC), containing a fragment from the signal recognition particle (SRP) RNA (domain IV) of Escherichia coli, has been determined at 1.7 A resolution with 21 666 independent reflections and an R(work) and R(free) of 20 ...

    The crystal structure of an RNA dodecamer, r(GCGUCAGGUC(Br)CG)/r(CGGAAGCAG(Br)CGC), containing a fragment from the signal recognition particle (SRP) RNA (domain IV) of Escherichia coli, has been determined at 1.7 A resolution with 21 666 independent reflections and an R(work) and R(free) of 20.1 and 22.5%, respectively. The structure exhibits a novel crystal packing pattern for RNA oligomer duplexes: one end of the duplex adopts the stacking interaction, while the other end adopts the abutting interaction in the minor groove. The symmetric loop of the SRP, r(CAGG)/r(AGCA), in the center of the dodecamer forms two different conformations of the A.C mismatch, a sheared G.G and a symmetrical G.A mismatch. These four mismatches present a unique surface for the abutting interaction. The involvement of the two A.C mismatches in the abutting interaction implies that these mismatches are the important sites for interaction with proteins. The conformation of the symmetric loop is greatly stabilized by hydrated metal ions, which display flexibility in adjusting their geometry and coordination in interaction with nucleic acids. Comparison with other crystal structures of fragments of 4.5S RNA indicates that the conformation of the symmetric loop is independent of the asymmetrical loop in domain IV.


    Organizational Affiliation

    Department of Chemistry, The Ohio State University, 200 Johnston Laboratory, 176 West 19th Avenue, Columbus, Ohio 43210, USA.



Macromolecules

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Entity ID: 1
MoleculeChainsLengthOrganismImage
5'-R(*GP*CP*GP*UP*CP*AP*GP*GP*UP*CP*(CBV)P*G)-3'A 12N/A
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsLengthOrganismImage
5'-R(*CP*GP*GP*AP*AP*GP*CP*AP*GP*(CBV)P*GP*C)-3'B 12N/A
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.200 
  • Space Group: P 43 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 35.61α = 90
b = 35.61β = 90
c = 133.96γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
CNSrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-06-03
    Type: Initial release
  • Version 1.1: 2008-04-28
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2011-11-02
    Changes: Non-polymer description