PDBsum entry 1p47

Transcription/DNA

PDB id: 1p47

Contents

Protein chains

87 a.a. *

DNA/RNA

Metals

_ZN ×6

Waters ×100

* Residue conservation analysis

PDB id:

1p47

Name:

Transcription/DNA

Title:

Crystal structure of tandem zif268 molecules complexed to DNA

Structure:

5'-d( Gp Tp Gp Gp Cp Gp Tp Gp Gp Gp Cp Gp Gp Cp Gp Tp Gp Gp Gp Cp Gp T)-3'. Chain: c. Engineered: yes. 5'-d( Cp Ap Cp Gp Cp Cp Cp Ap Cp Gp Cp Cp Gp Cp Cp Cp Ap Cp Gp Cp Cp A)-3'. Chain: d. Engineered: yes. Early growth response protein 1.

Source:

Synthetic: yes. Other_details: synthesized DNA oligo. Mus musculus. House mouse. Organism_taxid: 10090. Gene: egr1 or egr-1 or krox-24. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Biol. unit:

Tetramer (from PQS)

Resolution:

2.20Å R-factor: 0.219 R-free: 0.267

Authors:

E.Peisach,C.O.Pabo

Key ref:

E.Peisach and C.O.Pabo (2003). Constraints for zinc finger linker design as inferred from X-ray crystal structure of tandem Zif268-DNA complexes. J Mol Biol, 330, 1-7. PubMed id: 12818197 DOI: 10.1016/S0022-2836(03)00572-2

Date:

21-Apr-03 Release date: 24-Jun-03

Protein chains

P08046  (EGR1_MOUSE) -  Early growth response protein 1 from Mus musculus

Seq: 533 a.a.

Struc: 87 a.a.

DNA/RNA chains

G-T-G-G-C-G-T-G-G-G-C-G-G-C-G-T-G-G-G-C-G-T 22 bases

C-A-C-G-C-C-C-A-C-G-C-C-G-C-C-C-A-C-G-C-C-A 22 bases

DOI no: 10.1016/S0022-2836(03)00572-2

J Mol Biol 330:1-7 (2003)

PubMed id: 12818197

Constraints for zinc finger linker design as inferred from X-ray crystal structure of tandem Zif268-DNA complexes.

E.Peisach, C.O.Pabo.

ABSTRACT

Zinc-finger proteins offer a versatile and effective framework for the recognition of DNA binding sites. By connecting multiple fingers together with canonical TGEKP linkers, a protein may be designed to recognize almost any desired target DNA sequence. However, proteins containing more than three zinc-fingers do not bind as tightly as one might predict, and it appears that some type of strain is introduced when a six-finger protein is constructed with canonical linkers. In an attempt to understand the sources of this strain, we have solved the 2.2A resolution X-ray crystallographic structure of a complex that has two copies of the three-finger Zif268 protein bound to adjacent sites on one duplex DNA. Conceptually, this is equivalent to a six-finger protein in which the central linker has been removed and the complex has been allowed to "relax" to its most stable conformation. As in other Zif268-DNA complexes, the DNA is approximately linear and is slightly underwound. Surprisingly, the structure of the complex is similar (within 0.5A) to an arrangement that would allow a canonical linker at the center of the complex, and it seems possible that entropic effects (involving the librational degrees of freedom in the complex) could be important in determining optimal linker length.

Selected figure(s)

Figure 2.
Figure 2. Model of two Zif268 molecules bound to tandem binding sites. Fingers 1-3 are bound right to left. Fingers 1, 2 and 3 are colored in magenta, yellow, and orange, respectively. The red line indicates the gap for which a linker would be designed.

Figure 3.
Figure 3. Alignment of the first finger of Zif268 protein from the 1.6 Å 1AAY structure with the third finger of molecule A. The 1AAY structure is in cyan. The DNA in this structure is represented in green and only the region from Thy7 to Thy16 of the primary strand is shown. Finger 3 of molecule A is in orange, the first and second fingers of molecule B are in magenta and yellow.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2003, 330, 1-7) copyright 2003.

Figures were selected by an automated process.