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 

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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
  • Primary Citation of Related Structures:  
    3GUT

  • 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 nuclear factor kappaB (NF-kappaB) that becomes activated in virus-infected cells ...

    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

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Transcription factor p65A, C, E, G273Homo sapiensMutation(s): 0 
Gene Names: RELA, NFKB3
UniProt & NIH Common Fund Data Resources
Find proteins for Q04206 (Homo sapiens)
Explore Q04206 
Go to UniProtKB:  Q04206
PHAROS:  Q04206
GTEx:  ENSG00000173039 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ04206
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Nuclear factor NF-kappa-B p105 subunitB, D, F, H312Homo sapiensMutation(s): 0 
Gene Names: NFKB1
UniProt & NIH Common Fund Data Resources
Find proteins for P19838 (Homo sapiens)
Explore P19838 
Go to UniProtKB:  P19838
PHAROS:  P19838
GTEx:  ENSG00000109320 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP19838
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Entity ID: 3
MoleculeChainsLengthOrganismImage
HIV-LTR Core Forward StrandK [auth I],
I [auth X]		26Human immunodeficiency virus
Protein Feature View
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Entity ID: 4
MoleculeChainsLengthOrganismImage
HIV-LTR Core Reverse StrandL [auth J],
J [auth Y]		26Human immunodeficiency virus
Protein Feature View
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  • Reference Sequence
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  (Full details and data files)

  • 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