PDBsum entry: 1ci6

Transcription

PDB id: 1ci6

Contents

Protein chains

56 a.a. *

47 a.a. *

Ligands

BME

Metals

_FE ×3

Waters ×86

* Residue conservation analysis

PDB id:

1ci6

Name:

Transcription

Title:

Transcription factor atf4-c/ebp beta bzip heterodimer

Structure:

Transcription factor atf-4. Chain: a. Engineered: yes. Transcription factor c/ebp beta. Chain: b. Engineered: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008. Expression_system_variant: de3. Mus musculus. House mouse. Organism_taxid: 10090.

Biol. unit:

Tetramer (from PQS)

Resolution:

2.60Å R-factor: 0.217 R-free: 0.273

Authors:

L.M.Podust,Y.Kim

Key ref:

L.M.Podust et al. (2001). Crystal structure of the CCAAT box/enhancer-binding protein beta activating transcription factor-4 basic leucine zipper heterodimer in the absence of DNA. J Biol Chem, 276, 505-513. PubMed id: 11018027 DOI: 10.1074/jbc.M005594200

Date:

07-Apr-99 Release date: 04-Dec-00

Protein chain

P18848  (ATF4_HUMAN) -  Cyclic AMP-dependent transcription factor ATF-4

Seq: 351 a.a.

Struc: 56 a.a.

Protein chain

P28033  (CEBPB_MOUSE) -  CCAAT/enhancer-binding protein beta

Seq: 296 a.a.

Struc: 47 a.a.

 Gene Ontology (GO) functional annotation 

• Cellular component: nucleus (1 term)
• Biological process: regulation of transcription, DNA-dependent (1 term)
• Biochemical function: transcription factor activity (3 terms)

DOI no: 10.1074/jbc.M005594200

J Biol Chem 276:505-513 (2001)

PubMed id: 11018027

Crystal structure of the CCAAT box/enhancer-binding protein beta activating transcription factor-4 basic leucine zipper heterodimer in the absence of DNA.

L.M.Podust, A.M.Krezel, Y.Kim.

ABSTRACT

The crystal structure of the heterodimer formed by the basic leucine zipper (bZIP) domains of activating transcription factor-4 (ATF4) and CCAAT box/enhancer-binding protein beta (C/EBP beta), from two different bZIP transcription factor families, has been determined and refined to 2.6 A. The structure shows that the heterodimer forms an asymmetric coiled-coil. Even in the absence of DNA, the basic region of ATF4 forms a continuous alpha-helix, but the basic region of C/EBP beta is disordered. Proteolysis, electrophoretic mobility shift assay, circular dichroism, and NMR analyses indicated that (i) the bZIP domain of ATF4 is a disordered monomer and forms a homodimer upon binding to the DNA target; (ii) the bZIP domain of ATF4 forms a heterodimer with the bZIP domain of C/EBP beta that binds the cAMP response element, but not CCAAT box DNA, with high affinity; and (iii) the basic region of ATF4 has a higher alpha-helical propensity than that of C/EBP beta. These results suggest that the degree of ordering of the basic region and the fork and the dimerization properties of the leucine zipper combine to distinguish the structurally similar bZIP domains of ATF4 and C/EBP beta with respect to DNA target sequence. This study provides insight into the mechanism by which dimeric bZIP transcription factors discriminate between closely related but distinct DNA targets.

Selected figure(s)

Figure 1.
Fig. 1. Structure and interface of the C/EBP ·ATF4 heterodimer. A, the curved C/EBP helix wraps around the straight ATF4 helix. The structure of the heterodimer is shown in two views, related by 90° rotation about the axis perpendicular to the left-hand superhelical axis in the plane of drawing. The locations of the basic region, fork, and leucine zipper region are indicated. B, sequence alignment of the C/EBP and ATF4 bZIP domains. The residue numbers are as in the full-length proteins. The residues making direct contacts with DNA bases are shown in boldface. The pairwise intra- and interhelical interactions are summarized. The residues that make interactions are connected by solid lines. The distances between interacting intrahelical atoms are indicated above each line. The distances for residues making electrostatic interactions are boxed. C, a helical wheel diagram of the C/EBP ·ATF4 coiled-coil. Amino acids in the -helices are indicated in single-letter code. The coiled-coil sequence is read from N to C termini outwards from the wheel. Solid arrows indicate electrostatic interactions between the e and g positions. Dashed arrows indicate hydrogen bond interactions. The distances between interacting interhelical atoms are indicated above the arrows. D, potential interactions on homodimer interfaces of C/EBP and ATF4. Electrostatic attractive interactions are indicated by solid arrows; electrostatic repulsive interactions are indicated by solid lines; and hydrogen bond interactions are indicated by dashed arrows.

Figure 2.
Fig. 2. bZIP -helices. A, electron density of the ATF4 basic region from the 2F[o] F[c] map contoured at 1.0 . Intrahelical hydrogen bonds in the ATF4 fork-basic region junction formed between ATF4 Tyr295 and Lys299 as well as between ATF4 Gln297 and Arg300 contribute to the stability of the -helical conformation in the fork and the basic region. Dashed lines indicate the distances between water molecules and respective atoms of the side chains. The symmetry-related ATF4* molecule is shown in red. B, comparison of -helices. The ideal (gray) -helix was generated using insightII. Each bZIP domain was superimposed on the ideal -helix. The ATF4 bZIP domain is indicated in red, the C/EBP bZIP domain in the heterodimer in green, and the C/EBP bZIP domain in the C/EBP ·DNA complex in yellow-green. C, the potential disulfide bond in the ATF4 bZIP homodimer. The second subunit of the ATF4 bZIP dimer was generated by superimposing the bZIP domain of ATF4 in the heterodimer on the bZIP domain of C/EBP in the same heterodimer structure.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2001, 276, 505-513) copyright 2001.

Figures were selected by an automated process.