PDBsum entry: 2i9t

Transcription/DNA

PDB id: 2i9t

Contents

Protein chains

275 a.a. *

312 a.a. *

DNA/RNA

Waters ×21

* Residue conservation analysis

PDB id:

2i9t

Name:

Transcription/DNA

Title:

Structure of nf-kb p65-p50 heterodimer bound to prdii element of b-interferon promoter

Structure:

5'- d( Ap Gp Tp Gp Gp Gp Ap Ap Ap Tp Tp Cp Cp Tp Cp Tp G)-3'. Chain: c. Engineered: yes. Other_details: prdii DNA element. 5'- d( Cp Ap Gp Ap Gp Gp Ap Ap Tp Tp Tp Cp Cp Cp Ap Cp T)-3'. Chain: d. Engineered: yes.

Source:

Synthetic: yes. Mus musculus. House mouse. Organism_taxid: 10090. Gene: rela, nfkb3. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008. Gene: nfkb1.

Resolution:

2.80Å R-factor: 0.233 R-free: 0.288

Authors:

C.R Escalante,L.Shen,D.Thanos,A.K.Aggarwal

Key ref:

C.R.Escalante et al. (2002). Structure of NF-kappaB p50/p65 heterodimer bound to the PRDII DNA element from the interferon-beta promoter. Structure, 10, 383-391. PubMed id: 12005436 DOI: 10.1016/S0969-2126(02)00723-2

Date:

06-Sep-06 Release date: 06-Feb-07

Protein chain

Q04207  (TF65_MOUSE) -  Transcription factor p65

Seq: 549 a.a.

Struc: 275 a.a.*

Protein chain

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

Seq: 971 a.a.

Struc: 312 a.a.

* PDB and UniProt seqs differ at 2 residue positions (black crosses)

 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: 10.1016/S0969-2126(02)00723-2

Structure 10:383-391 (2002)

PubMed id: 12005436

Structure of NF-kappaB p50/p65 heterodimer bound to the PRDII DNA element from the interferon-beta promoter.

C.R.Escalante, L.Shen, D.Thanos, A.K.Aggarwal.

ABSTRACT

Upon viral infection, NF-kappaB translocates to the nucleus and activates the IFN-beta gene by binding to the PRDII element. Strikingly, NF-kappaB loses its ability to activate the IFN-beta gene when the PRDII element is substituted by closely related sites. We report here the crystal structure of NF-kappaB p50/p65 heterodimer bound to the PRDII element from the IFN-beta promoter. The structure reveals an unexpected alteration in configuration, in which the p50 specificity domain moves by as much as approximately 9 A when compared to NF-kappaB heterodimer bound to the immunoglobulin kappaB site (Ig-kappaB) while maintaining the same base-specific contacts with the DNA. Taken together, the structure offers new insights into the allosteric effects of closely related DNA sites on the configuration of NF-kappaB and its transcriptional selectivity.

Selected figure(s)

Figure 2.
Figure 2. Overall View of the Structure
(A) Ribbon diagram of the p65/p50 heterodimer bound to the PRDII element, viewed down the DNA helical axis. The p50 subunit is shown in blue and the p65 subunit in red. The DNA is shown in gold. The secondary elements, loops, and N and C termini are labeled.
(B) Stereo representation of a Cα trace of the complex, with every twentieth residue labeled. Figure 2. Overall View of the Structure(A) Ribbon diagram of the p65/p50 heterodimer bound to the PRDII element, viewed down the DNA helical axis. The p50 subunit is shown in blue and the p65 subunit in red. The DNA is shown in gold. The secondary elements, loops, and N and C termini are labeled.(B) Stereo representation of a Cα trace of the complex, with every twentieth residue labeled.

Figure 5.
Figure 5. Comparison of van der Waals Interactions between Tyr57 and the Inner DNA Bases
(A) In the NF-κB[50/65]-PRDII structure, Tyr57 is shown interacting with the methyl groups of adjacent A:T base pairs.
(B) In the NF-κB[50/65]-Ig structure, the thymine of the single A:T base pair rolls and twists out of plane. Figure 5. Comparison of van der Waals Interactions between Tyr57 and the Inner DNA Bases(A) In the NF-κB[50/65]-PRDII structure, Tyr57 is shown interacting with the methyl groups of adjacent A:T base pairs.(B) In the NF-κB[50/65]-Ig structure, the thymine of the single A:T base pair rolls and twists out of plane.

The above figures are reprinted by permission from Cell Press: Structure (2002, 10, 383-391) copyright 2002.

Figures were selected by the author.