397D

A 1.3 A RESOLUTION CRYSTAL STRUCTURE OF THE HIV-1 TRANS-ACTIVATION RESPONSE REGION RNA STEM REVEALS A METAL ION-DEPENDENT BULGE CONFORMATION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free: 0.177 
  • R-Value Observed: 0.126 

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This is version 1.2 of the entry. See complete history


Literature

A 1.3-A resolution crystal structure of the HIV-1 trans-activation response region RNA stem reveals a metal ion-dependent bulge conformation.

Ippolito, J.A.Steitz, T.A.

(1998) Proc Natl Acad Sci U S A 95: 9819-9824

  • DOI: 10.1073/pnas.95.17.9819
  • Primary Citation of Related Structures:  
    397D

  • PubMed Abstract: 
  • The crystal structure of an HIV-1 trans-activation response region (TAR) RNA fragment containing the binding site for the trans-activation protein Tat has been determined to 1.3-A resolution. In this crystal structure, the characteristic UCU bulge of TAR adopts a conformation that is stabilized by three divalent calcium ions and differs from those determined previously by solution NMR ...

    The crystal structure of an HIV-1 trans-activation response region (TAR) RNA fragment containing the binding site for the trans-activation protein Tat has been determined to 1.3-A resolution. In this crystal structure, the characteristic UCU bulge of TAR adopts a conformation that is stabilized by three divalent calcium ions and differs from those determined previously by solution NMR. One metal ion, crucial to the loop conformation, binds directly to three phosphates in the loop region. The structure emphasizes the influence of metal ion binding on RNA structure and, given the abundance of divalent metal ion in the cell, raises the question of whether metal ions play a role in the conformation of TAR RNA and the interaction of TAR with Tat and cyclin T in vivo.


    Organizational Affiliation

    Department of Molecular Biophysics and Biochemistry,, New Haven, CT 06520-8114, USA.



Macromolecules

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Entity ID: 1
MoleculeChainsLengthOrganismImage
RNA (5'-R(*GP*GP*CP*CP*AP*GP*AP*UP*CP*UP*GP*AP*GP*CP*G)-3')A 15N/A
Protein Feature View
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  • Reference Sequence

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free: 0.177 
  • R-Value Observed: 0.126 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 27.1α = 69.2
b = 27.1β = 77.5
c = 31.6γ = 63
Software Package:
Software NamePurpose
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1998-09-11
    Type: Initial release
  • Version 1.1: 2008-05-22
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance