PDBsum entry 1rb5

DNA binding protein

PDB id: 1rb5

Contents

Protein chains

34 a.a.

33 a.a.

Waters ×189

PDB id:

1rb5

Name:

DNA binding protein

Title:

Antiparallel trimer of gcn4-leucine zipper core mutant as n16a trigonal form

Structure:

General control protein gcn4. Chain: a, b, c. Fragment: leucine-zipper (residues 249-281). Synonym: amino acid biosynthesis regulatory protein. Engineered: yes. Mutation: yes

Source:

Synthetic: yes. Other_details: the sequence of the protein is naturally found in saccharomyces cerevisiae. The protein was chemically synthesized.

Biol. unit:

Trimer (from PQS)

Resolution:

1.90Å R-factor: 0.205 R-free: 0.257

Authors:

J.Holton,T.Alber

Key ref:

J.Holton and T.Alber (2004). Automated protein crystal structure determination using ELVES. Proc Natl Acad Sci U S A, 101, 1537-1542. PubMed id: 14752198 DOI: 10.1073/pnas.0306241101

Date:

01-Nov-03 Release date: 13-Jan-04

Protein chains

P03069  (GCN4_YEAST) -  General control transcription factor GCN4 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 281 a.a.

Struc: 33 a.a.*

Protein chain

P03069  (GCN4_YEAST) -  General control transcription factor GCN4 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 281 a.a.

Struc: 32 a.a.*

* PDB and UniProt seqs differ at 2 residue positions (black crosses)

DOI no: 10.1073/pnas.0306241101

Proc Natl Acad Sci U S A 101:1537-1542 (2004)

PubMed id: 14752198

Automated protein crystal structure determination using ELVES.

J.Holton, T.Alber.

ABSTRACT

Efficient determination of protein crystal structures requires automated x-ray data analysis. Here, we describe the expert system ELVES and its use to determine automatically the structure of a 12-kDa protein. Multiwavelength anomalous diffraction analysis of a selenomethionyl derivative was used to image the Asn-16-Ala variant of the GCN4 leucine zipper. In contrast to the parallel, dimeric coiled coil formed by the WT sequence, the mutant unexpectedly formed an antiparallel trimer. This structural switch reveals how avoidance of core cavities at a single site can select the native fold of a protein. All structure calculations, including indexing, data processing, locating heavy atoms, phasing by multiwavelength anomalous diffraction, model building, and refinement, were completed without human intervention. The results demonstrate the feasibility of automated methods for determining high-resolution, x-ray crystal structures of proteins.

Selected figure(s)

Figure 2.
Fig. 2. Experimental, 1.8-Å resolution MAD-phased electron density map (P3[1]21, contoured at 1 ) produced by ELVES superimposed on the refined model of the GCN4 Asn-16-Ala leucine-zipper variant. (A) Cross section through the trimer at the level of the Ala-16-Leu-12-Leu-12 layer. (B) Cross section through the trimer at the level of the Leu-12-Ala-16-Ala-16 layer.

Figure 3.
Fig. 3. The Asn-16-Ala variant of the GCN4 leucine zipper forms an antiparallel, trimeric coiled coil. (A) Stereo ribbon diagram of the overall structure. Each helix is colored in increasingly cool colors from the amino to the carboxyl terminus. (B) Superpositions of the structures determined by automated (blue) and manual (yellow) methods in the trigonal (Left) and tetragonal (Right) crystal forms. (C) Cross section showing the Ala-16-Leu-12-Leu-12 layer with the van der Waals surfaces of the core amino acids filling the space in the core of the trimer. (D) Close packing of the Leu-12-Ala-16-Ala-16 layer. (E) In contrast, a 165-Å3 cavity exists in the Ala-16 layer of the parallel trimer stabilized by benzene (29).

Figures were selected by an automated process.