1LEI

The kB DNA sequence from the HLV-LTR functions as an allosteric regulator of HIV transcription


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.250 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The kB DNA sequence from the HIV Long Terminal Repeat functions as an allosteric regulator of HIV transcription

Chen-Park, F.E.Huang, D.B.Noro, B.Thanos, D.Ghosh, G.

(2002) J.Biol.Chem. 277: 24701-24708

  • DOI: 10.1074/jbc.M200007200

  • PubMed Abstract: 
  • NF-kappaB is an inducible transcription factor involved in the immune response, inflammation, and viral transcription. To address how the two NF-kappaB and three Sp1 binding sites of the human immunodeficiency virus (HIV) long terminal repeat (LTR) c ...

    NF-kappaB is an inducible transcription factor involved in the immune response, inflammation, and viral transcription. To address how the two NF-kappaB and three Sp1 binding sites of the human immunodeficiency virus (HIV) long terminal repeat (LTR) control multiple activator assembly and transcription, we first observed and compared unique conformations between the crystallographic structure of the NF-kappaB p50.p65 heterodimer bound to the uPA-kappaB target site to that of the p50.p65.HIV-kappaB complex. Next, cooperativity between two NF-kappaB molecules bound to tandem HIV-kappaB sequences was measured as well as that of NF-kappaB and transcription factor Sp1 when bound to adjacent sites. The cooperativity of hybrid HIV-LTR enhancers was measured with the 3' kappaB site converted to uPA-kappaB or to interferon beta gene enhancer kappaB. The hybrids were defective in transcriptional activator assembly and less active transcriptionally. These functional differences correlate with observed conformational differences and demonstrate that distinct kappaB DNA sequences function as allosteric regulators in a gene-specific manner.


    Organizational Affiliation

    Department of Biology, University of California, San Diego, La Jolla, California 92093-0359, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
NUCLEAR FACTOR NF-KAPPA-B P65 SUBUNIT
A
274Mus musculusGene Names: Rela (Nfkb3)
Find proteins for Q04207 (Mus musculus)
Go to UniProtKB:  Q04207
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
NUCLEAR FACTOR NF-KAPPA-B P50 SUBUNIT
B
313Mus musculusGene Names: Nfkb1
Find proteins for P25799 (Mus musculus)
Go to UniProtKB:  P25799
Entity ID: 1
MoleculeChainsLengthOrganism
5'-D(*CP*TP*CP*AP*GP*GP*GP*AP*AP*AP*GP*TP*AP*CP*AP*GP*A)-3'C17N/A
Entity ID: 2
MoleculeChainsLengthOrganism
5'-D(*TP*CP*TP*GP*5ITP*AP*CP*5ITP*5ITP*5ITP*CP*CP*CP*TP*GP*AP*G)-3'D17N/A
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
5IU
Query on 5IU
D
DNA LINKINGC9 H12 I N2 O8 PDU
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
DNAKd: 0.8 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.250 
  • Space Group: C 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 137.131α = 90.00
b = 179.697β = 90.00
c = 97.068γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
CNSrefinement
DENZOdata reduction
AMoREphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-04-15
    Type: Initial release
  • Version 1.1: 2008-04-28
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance