PDBsum entry: 1ooa

Transcription/RNA

PDB id: 1ooa

Contents

Protein chains

313 a.a. *

DNA/RNA

Waters ×294

* Residue conservation analysis

PDB id:

1ooa

Name:

Transcription/RNA

Title:

Crystal structure of nf-kb(p50)2 complexed to a high- affinity RNA aptamer

Structure:

RNA aptamer. Chain: c, d. Fragment: 29-nt RNA aptamer. Engineered: yes. Nuclear factor nf-kappa-b p105 subunit. Chain: a, b. Synonym: DNA-binding factor kbf1, ebp- 1, nf-kappa-b1 p84/nf-kappa-b1 p98, [contains: nuclear factor nf- kappa-b p50 subunit].

Source:

Synthetic: yes. Other_details: synthesis of the RNA fragment from the t7 promoter in vitro transcription. Mus musculus. House mouse. Organism_taxid: 10090. Gene: nfkb1. Expressed in: escherichia coli bl21. Expression_system_taxid: 511693.

Biol. unit:

Dimer (from PQS)

Resolution:

2.45Å R-factor: 0.208 R-free: 0.248

Authors:

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

Key ref:

D.B.Huang et al. (2003). Crystal structure of NF-kappaB (p50)2 complexed to a high-affinity RNA aptamer. Proc Natl Acad Sci U S A, 100, 9268-9273. PubMed id: 12886018 DOI: 10.1073/pnas.1632011100

Date:

03-Mar-03 Release date: 22-Jul-03

Protein chains

P25799  (NFKB1_MOUSE) -  Nuclear factor NF-kappa-B p105 subunit

Seq: 971 a.a.

Struc: 313 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

 Gene Ontology (GO) functional annotation 

• Cellular component: nucleus (1 term)
• Biological process: regulation of transcription (2 terms)
• Biochemical function: transcription factor activity (1 term)

DOI no: 10.1073/pnas.1632011100

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

PubMed id: 12886018

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

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

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 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.

Selected figure(s)

Figure 3.
Fig. 3. Structure of the RNA aptamer. (a) Overall structure of the -p50 RNA aptamer. Residues 1-15 representing one strand are cyan, and residues 16-29 representing the other strand are orange. (b) A close-up view of the folded structure of the internal loop. Three cross-strand-stacked guanines are indicated. The non-Watson-Crick hydrogen bond pairing between U6 and C^24 and between A^9 and G22 of the internal loop are indicated. (c) Surface presentation (23) of the RNA in two orientations related by 180° rotation around the long axis. The image on the left is in the same orientation as a and shows the narrow minor-groove section near the internal loop. The image on the right shows the protein-binding groove of the RNA.

Figure 5.
Fig. 5. The detailed chemistry of the RNA/p50 RHR complex interface. (a) Direct base-specific hydrogen-bonding contacts between p50 and the RNA aptamer at the core of the protein-RNA interface. (b) Direct base-specific hydrogen-bonding contacts between p50 and p50-specific DNA half site observed in the x-ray structure of p50 homodimer bound to MHC- B DNA. (c) Stacking interactions between residues in the linker (P243 and K241) and RNA bases (G8 and G22) shown by van der Waals surface model. (d) Contacts between p50 and RNA along one side of the RNA duplex. Nonspecific RNA backbone contacts by the protein are highlighted in three places of the RNA aptamer. Protein residues in yellow denote specific contacts.

Figures were selected by the author.