1OOA

CRYSTAL STRUCTURE OF NF-kB(p50)2 COMPLEXED TO A HIGH-AFFINITY RNA APTAMER

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.208 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history. 


Literature

Crystal structure of NF-kappaB (p50)2 complexed to a high-affinity RNA aptamer.

Huang, D.B., Vu, D., Cassiday, L.A., Zimmerman, J.M., Maher III, L.J., Ghosh, G.

(2003) Proc Natl Acad Sci U S A 100: 9268-9273

  • DOI: 10.1073/pnas.1632011100
  • Structures With Same Primary Citation

  • PubMed Abstract: 

    • We have recently identified an RNA aptamer for the transcription factor NF-kappaB p50 homodimer [(p50)2], which exhibits little sequence resemblance to the consensus DNA target for (p50)2, but binds (p50)2 with an affinity similar to that of the optimal DNA target ...

    We have recently identified an RNA aptamer for the transcription factor NF-kappaB p50 homodimer [(p50)2], which exhibits little sequence resemblance to the consensus DNA target for (p50)2, but binds (p50)2 with an affinity similar to that of the optimal DNA target. We describe here the 2.45-A resolution x-ray crystal structure of the p50 RHR/RNA aptamer complex. The structure reveals that two RNA molecules bind independent of each other to the p50 N-terminal Ig-like domains. The RNA secondary structure is comprised of a stem and a stem-loop separated by an internal loop folded into a kinked helix because of the cross-strand stacking of three internal loop guanines. These guanines, placed at the edge of the 3' helix, together with the major groove of the irregular 3' helix, form the binding surface for p50. Each p50 monomer uses the same surface to recognize the distorted RNA major groove as observed in the kappaB DNA/p50 RHR complex, resulting in strikingly similar interfaces. The structure reveals how the aptamer specifically selects p50 and discriminates against p65. We also discuss the physiological implications of RNA binding by (p50)2.

    Organizational Affiliation: 

    Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, CA 93092-0359, USA.



Macromolecules

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Nuclear factor NF-kappa-B p105 subunitA, B326Mus musculusMutation(s): 0 
Gene Names: Nfkb1
Find proteins for P25799 (Mus musculus)
Explore P25799 
Go to UniProtKB:  P25799
NIH Common Fund Data Resources
IMPC  MGI:97312
Protein Feature View
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  • Reference Sequence

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Entity ID: 1
MoleculeChainsLengthOrganism
RNA aptamerC, D29N/A
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.208 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 76.753α = 90
b = 151.059β = 105.95
c = 95.628γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
HKL-2000data reduction

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-07-22
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance