PDBsum entry 1a1h

Transcription/DNA

PDB id: 1a1h

Contents

Protein chain

85 a.a. *

DNA/RNA

Metals

_ZN ×3

Waters ×149

* Residue conservation analysis

PDB id:

1a1h

Name:

Transcription/DNA

Title:

Qgsr (zif268 variant) zinc finger-DNA complex (gcac site)

Structure:

DNA (5'-d( Ap Gp Cp Gp Tp Gp Gp Gp Cp Ap C)-3'). Chain: b. Engineered: yes. DNA (5'-d( Tp Gp Tp Gp Cp Cp Cp Ap Cp Gp C)-3'). Chain: c. Engineered: yes. Qgsr zinc finger peptide. Chain: a. Engineered: yes

Source:

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

Resolution:

1.60Å R-factor: 0.235 R-free: 0.277

Authors:

M.Elrod-Erickson,T.E.Benson,C.O.Pabo

Key ref:

M.Elrod-Erickson et al. (1998). High-resolution structures of variant Zif268-DNA complexes: implications for understanding zinc finger-DNA recognition. Structure, 6, 451-464. PubMed id: 9562555 DOI: 10.1016/S0969-2126(98)00047-1

Date:

10-Dec-97 Release date: 10-Jun-98

Protein chain

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

Seq: 533 a.a.

Struc: 85 a.a.*

* PDB and UniProt seqs differ at 3 residue positions (black crosses)

DNA/RNA chains

A-G-C-G-T-G-G-G-C-A-C 11 bases

T-G-T-G-C-C-C-A-C-G-C 11 bases

Enzyme reactions

• Enzyme class: E.C.?

DOI no: 10.1016/S0969-2126(98)00047-1

Structure 6:451-464 (1998)

PubMed id: 9562555

High-resolution structures of variant Zif268-DNA complexes: implications for understanding zinc finger-DNA recognition.

M.Elrod-Erickson, T.E.Benson, C.O.Pabo.

ABSTRACT

BACKGROUND: Zinc fingers of the Cys2-His2 class comprise one of the largest families of eukaryotic DNA-binding motifs and recognize a diverse set of DNA sequences. These proteins have a relatively simple modular structure and key base contacts are typically made by a few residues from each finger. These features make the zinc finger motif an attractive system for designing novel DNA-binding proteins and for exploring fundamental principles of protein-DNA recognition. RESULTS: Here we report the X-ray crystal structures of zinc finger-DNA complexes involving three variants of Zif268, with multiple changes in the recognition helix of finger one. We describe the structure of each of these three-finger peptides bound to its corresponding target site. To help elucidate the differential basis for site-specific recognition, the structures of four other complexes containing various combinations of these peptides with alternative binding sites have also been determined. CONCLUSIONS: The protein-DNA contacts observed in these complexes reveal the basis for the specificity demonstrated by these Zif268 variants. Many, but not all, of the contacts can be rationalized in terms of a recognition code, but the predictive value of such a code is limited. The structures illustrate how modest changes in the docking arrangement accommodate the new sidechain-base and sidechain-phosphate interactions. Such adaptations help explain the versatility of naturally occurring zinc finger proteins and their utility in design.

Selected figure(s)

Figure 4.
Figure 4. Stereo view of the contacts made by finger one in the complex between (a) the RADR peptide and the targeted GCAC binding site, (b) the RADR peptide and the wild-type GCGT binding site, (c) the RADR peptide and the GACC binding site, and (d) the wild-type Zif268 peptide and the GCAC binding site. The sidechains of residues 18, 20, 21 and 24 (positions -1, 2, 3 and 6 of the a helix) and the peptide backbone are shown in gold for the RADR peptide, with alternate conformations indicated in gray. The wild-type peptide is shown in magenta, with alternate conformations indicated in gray. Water molecules are represented as spheres; only those water molecules that mediate interactions between the peptide and base pairs 8-10 are shown. The DNA is color-coded by strand, with the primary strand in purple and the secondary strand in blue. Fingers two and three are not shown. (The figure was made with the program SETOR [30].)

The above figure is reprinted by permission from Cell Press: Structure (1998, 6, 451-464) copyright 1998.

Figure was selected by an automated process.