PDBsum entry 2o61

Transcription/DNA

PDB id: 2o61

Contents

Protein chains

498 a.a. *

314 a.a. *

DNA/RNA

Waters ×25

* Residue conservation analysis

PDB id:

2o61

Name:

Transcription/DNA

Title:

Crystal structure of nfkb, irf7, irf3 bound to the interferon-b enhancer

Structure:

36-mer. Chain: e. Engineered: yes. 34-mer. Chain: f. Engineered: yes. Transcription factor p65/interferon regulatory factor 7/interferon regulatory factor 3 fusion protein. Chain: a.

Source:

Synthetic: yes. Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli. Expression_system_taxid: 562. Gene: nfkb1. Expression_system_taxid: 562

Resolution:

2.80Å R-factor: 0.245 R-free: 0.278

Authors:

D.Panne

Key ref:

D.Panne et al. (2007). An atomic model of the interferon-beta enhanceosome. Cell, 129, 1111-1123. PubMed id: 17574024 DOI: 10.1016/j.cell.2007.05.019

Date:

06-Dec-06 Release date: 24-Jul-07

Protein chain

Q04206  (TF65_HUMAN) -  Transcription factor p65 from Homo sapiens

Seq: 551 a.a.

Struc: 498 a.a.*

Protein chain

Q14653  (IRF3_HUMAN) -  Interferon regulatory factor 3 from Homo sapiens

Seq: 427 a.a.

Struc: 498 a.a.*

Protein chain

Q92985  (IRF7_HUMAN) -  Interferon regulatory factor 7 from Homo sapiens

Seq: 503 a.a.

Struc: 498 a.a.*

Protein chain

P19838  (NFKB1_HUMAN) -  Nuclear factor NF-kappa-B p105 subunit from Homo sapiens

Seq: 968 a.a.

Struc: 314 a.a.*

* PDB and UniProt seqs differ at 333 residue positions (black crosses)

DNA/RNA chains

T-T-G-A-A-A-G-G-G-A-G-A-A-G-T-G-A-A-A-G-T-G-G-G-A-A-A-T-T-C-C-T-C-T-G-T 36 bases

C-A-G-A-G-G-A-A-T-T-T-C-C-C-A-C-T-T-T-C-A-C-T-T-C-T-C-C-C-T-T-T-C-A 34 bases

DOI no: 10.1016/j.cell.2007.05.019

Cell 129:1111-1123 (2007)

PubMed id: 17574024

An atomic model of the interferon-beta enhanceosome.

D.Panne, T.Maniatis, S.C.Harrison.

ABSTRACT

Transcriptional activation of the interferon-beta (IFN-beta) gene requires assembly of an enhanceosome containing ATF-2/c-Jun, IRF-3/IRF-7, and NFkappaB. These factors bind cooperatively to the IFN-beta enhancer and recruit coactivators and chromatin-remodeling proteins to the IFN-beta promoter. We describe here a crystal structure of the DNA-binding domains of IRF-3, IRF-7, and NFkappaB, bound to one half of the enhancer, and use a previously described structure of the remaining half to assemble a complete picture of enhanceosome architecture in the vicinity of the DNA. Association of eight proteins with the enhancer creates a continuous surface for recognizing a composite DNA-binding element. Paucity of local protein-protein contacts suggests that cooperative occupancy of the enhancer comes from both binding-induced changes in DNA conformation and interactions with additional components such as CBP. Contacts with virtually every nucleotide pair account for the evolutionary invariance of the enhancer sequence.

Selected figure(s)

Figure 2.
Figure 2. Structure of the NFκB:IRF-7:IRF-3:DNA Complex
Ribbons representation of the complex viewed (A) normal to and (B) along the DNA helical axis. The RHR of p50 is in light blue, and that of RelA in dark blue. IRF-7D is in yellow, and IRF-3C in green. The two DNA strands are in gray. (C) Sequence of the DNA duplex corresponding to the PRDI-II region of the IFN-β enhancer (−85 to −51 nucleotides from the start site of transcription). (D) Protein-DNA contacts of IRF-3C. (E) Protein-DNA contacts of IRF-7D.

Figure 3.
Figure 3. Protein-DNA Contacts
Schematic diagram of protein-DNA contacts generated with NUCPLOT (Luscombe et al., 1997). Residues from ATF-2 are in red, c-Jun in dark red, IRF-3A and C in green, and IRF-7B and D in yellow. The RHR of p50 is in light blue, and that of RelA in dark blue. The core binding sites for each protein are indicated in the corresponding colors. Blue lines indicate hydrogen bonds, red lines, van der Waals contacts.

The above figures are reprinted from an Open Access publication published by Cell Press: Cell (2007, 129, 1111-1123) copyright 2007.

Figures were selected by an automated process.