3GUT

Crystal structure of a higher-order complex of p50:RelA bound to the HIV-1 LTR


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.59 Å
  • R-Value Free: 0.301 
  • R-Value Work: 0.245 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural basis of HIV-1 activation by NF-kappaB--a higher-order complex of p50:RelA bound to the HIV-1 LTR.

Stroud, J.C.Oltman, A.Han, A.Bates, D.L.Chen, L.

(2009) J Mol Biol 393: 98-112

  • DOI: 10.1016/j.jmb.2009.08.023
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • The activation and latency of human immunodeficiency virus type 1 (HIV-1) are tightly controlled by the transcriptional activity of its long terminal repeat (LTR) region. The LTR is regulated by viral proteins as well as host factors, including the n ...

    The activation and latency of human immunodeficiency virus type 1 (HIV-1) are tightly controlled by the transcriptional activity of its long terminal repeat (LTR) region. The LTR is regulated by viral proteins as well as host factors, including the nuclear factor kappaB (NF-kappaB) that becomes activated in virus-infected cells. The two tandem NF-kappaB sites of the LTR are among the most highly conserved sequence elements of the HIV-1 genome. Puzzlingly, these sites are arranged in a manner that seems to preclude simultaneous binding of both sites by NF-kappaB, although previous biochemical work suggests otherwise. Here, we have determined the crystal structure of p50:RelA bound to the tandem kappaB element of the HIV-1 LTR as a dimeric dimer, providing direct structural evidence that NF-kappaB can occupy both sites simultaneously. The two p50:RelA dimers bind the adjacent kappaB sites and interact through a protein contact that is accommodated by DNA bending. The two dimers clamp DNA from opposite faces of the double helix and form a topological trap of the bound DNA. Consistent with these structural features, our biochemical analyses indicate that p50:RelA binds the HIV-1 LTR tandem kappaB sites with an apparent anti-cooperativity but enhanced kinetic stability. The slow on and off rates we observe may be relevant to viral latency because viral activation requires sustained NF-kappaB activation. Furthermore, our work demonstrates that the specific arrangement of the two kappaB sites on the HIV-1 LTR can modulate the assembly kinetics of the higher-order NF-kappaB complex on the viral promoter. This phenomenon is unlikely restricted to the HIV-1 LTR but probably represents a general mechanism for the function of composite DNA elements in transcription.


    Organizational Affiliation

    Molecular and Computational Biology, Department of Biological Sciences, Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90089-2910, USA.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Transcription factor p65
A, C, E, G
273Homo sapiensMutation(s): 0 
Gene Names: RELANFKB3
Find proteins for Q04206 (Homo sapiens)
Go to UniProtKB:  Q04206
NIH Common Fund Data Resources
PHAROS  Q04206

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Nuclear factor NF-kappa-B p105 subunit
B, D, F, H
312Homo sapiensMutation(s): 0 
Gene Names: NFKB1
Find proteins for P19838 (Homo sapiens)
Go to UniProtKB:  P19838
NIH Common Fund Data Resources
PHAROS  P19838

Find similar nucleic acids by: Sequence  |  Structure

Entity ID: 4
MoleculeChainsLengthOrganism
HIV-LTR Core Reverse StrandJ, Y26Human immunodeficiency virus

Find similar nucleic acids by: Sequence  |  Structure

Entity ID: 3
MoleculeChainsLengthOrganism
HIV-LTR Core Forward StrandI, X26Human immunodeficiency virus
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.59 Å
  • R-Value Free: 0.301 
  • R-Value Work: 0.245 
  • Space Group: P 42
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 167.493α = 90
b = 167.493β = 90
c = 172.757γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACTdata extraction
ADSCdata collection
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-09-08
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-11-01
    Changes: Refinement description