PDBsum entry: 2o93

Transcription/DNA

PDB id: 2o93

Contents

Protein chains

287 a.a. *

DNA/RNA

* Residue conservation analysis

PDB id:

2o93

Name:

Transcription/DNA

Title:

Crystal structure of nfat bound to the HIV-1 ltr tandem kappab enhancer element

Structure:

Kappab enhancer element, DNA 25-mer. Chain: a. Engineered: yes. Kappab enhancer element, DNA 25-mer. Chain: b. Engineered: yes. Actor of activated t-cells, cytoplasmic 2. Chain: l, m, o. Fragment: rhr domain.

Source:

Synthetic: yes. Homo sapiens. Human. Organism_taxid: 9606. Gene: nfatc2, nfat1, nfatp. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

3.05Å R-factor: 0.225 R-free: 0.283

Authors:

D.L.Bates,L.Chen

Key ref:

D.L.Bates et al. (2008). Crystal structure of NFAT bound to the HIV-1 LTR tandem kappaB enhancer element. Structure, 16, 684-694. PubMed id: 18462673 DOI: 10.1016/j.str.2008.01.020

Date:

13-Dec-06 Release date: 19-Jun-07

Protein chains

Q13469  (NFAC2_HUMAN) -  Nuclear factor of activated T-cells, cytoplasmic 2

Seq: 925 a.a.

Struc: 287 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/j.str.2008.01.020

Structure 16:684-694 (2008)

PubMed id: 18462673

Crystal structure of NFAT bound to the HIV-1 LTR tandem kappaB enhancer element.

D.L.Bates, K.K.Barthel, Y.Wu, R.Kalhor, J.C.Stroud, M.J.Giffin, L.Chen.

ABSTRACT

The host factor, nuclear factor of activated T-cells (NFAT), regulates the transcription and replication of HIV-1. Here, we have determined the crystal structure of the DNA binding domain of NFAT bound to the HIV-1 long terminal repeat (LTR) tandem kappaB enhancer element at 3.05 A resolution. NFAT binds as a dimer to the upstream kappaB site (Core II), but as a monomer to the 3' end of the downstream kappaB site (Core I). The DNA shows a significant bend near the 5' end of Core I, where a lysine residue from NFAT bound to the 3' end of Core II inserts into the minor groove and seems to cause DNA bases to flip out. Consistent with this structural feature, the 5' end of Core I become hypersensitive to dimethylsulfate in the in vivo footprinting upon transcriptional activation of the HIV-1 LTR. Our studies provide a basis for further investigating the functional mechanisms of NFAT in HIV-1 transcription and replication.

Selected figure(s)

Figure 4.
Figure 4. DNA conformation of the HIV-1 LTR tandem κB sites
(A) A simulated omit map (contour level 2σ) showing well-defined density of the HIV-1 LTR tandem κB sites and the distorted DNA helix. The sequence of the top strand is labeled.
(B) Superposition of the DNA in the crystal (dark cyan) and an ideal B-DNA containing the sequence of the HIV-1 LTR tandem κB sites (magenta) shows that the DNA bend is located at the 5′ end of Core I.

Figure 6.
Figure 6. Schematic of Interactions between NFAT and the HIV-1 LTR Tandem κB Sites
DNA is represented as a ladder, with bases as ovals and labeled according to the text and Figure 1A. The backbone phosphates are represented as circles, with the letter P inside. “Monomer” represents the NFAT molecule bound to the 3′ end of Core I, the residues of which are colored ruby red. “Dimer 2” represents the NFAT molecule bound to the 3′ end of Core II, the residues of which are colored deep purple. “Dimer 1” represents the NFAT molecule bound to the 5′ end of Core II, the residues of which are colored deep blue. Hydrogen bonding interactions are represented by solid arrows, while van der Waals interactions are represented by dashed arrows. The guanine nucleotides protected in the in vivo DMS footprinting are highlighted by bold, dashed ellipses, whereas guanine residues with enhanced reactivity toward DMS are highlighted by bold, red ellipses. For clarity, only representative protein-DNA contacts are shown in the figure.

The above figures are reprinted from an Open Access publication published by Cell Press: Structure (2008, 16, 684-694) copyright 2008.

Figures were selected by the author.