PDBsum entry 1mph

Signal transduction

PDB id: 1mph

Contents

Protein chain

106 a.a. *

* Residue conservation analysis

PDB id:

1mph

Name:

Signal transduction

Title:

Pleckstrin homology domain from mouse beta-spectrin, nmr, 50 structures

Structure:

Beta spectrin. Chain: a. Fragment: pleckstrin homology. Synonym: ph domain. Engineered: yes

Source:

Mus musculus. House mouse. Organism_taxid: 10090. Cell_line: bl21. Organ: brain. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

NMR struc:

50 models

Authors:

M.Nilges,M.J.Macias,S.I.O'Donoghue,H.Oschkinat

Key ref:

M.Nilges et al. (1997). Automated NOESY interpretation with ambiguous distance restraints: the refined NMR solution structure of the pleckstrin homology domain from beta-spectrin. J Mol Biol, 269, 408-422. PubMed id: 9199409 DOI: 10.1006/jmbi.1997.1044

Date:

23-Apr-97 Release date: 16-Jun-97

Protein chain

Q62261  (SPTB2_MOUSE) -  Spectrin beta chain, non-erythrocytic 1 from Mus musculus

Seq: 2363 a.a.

Struc: 106 a.a.

DOI no: 10.1006/jmbi.1997.1044

J Mol Biol 269:408-422 (1997)

PubMed id: 9199409

Automated NOESY interpretation with ambiguous distance restraints: the refined NMR solution structure of the pleckstrin homology domain from beta-spectrin.

M.Nilges, M.J.Macias, S.I.O'Donoghue, H.Oschkinat.

ABSTRACT

We have used a novel, largely automated, calculation method to refine the NMR solution structure of the pleckstrin homology domain of beta-spectrin. The method is called ARIA for Ambiguous Restraints for Iterative Assignment. The starting point for ARIA is an almost complete assignment of the proton chemical shifts, and a list of partially assigned NOEs, mostly sequential and secondary structure NOEs. The restraint list is then augmented by automatically interpreting peak lists generated by automated peak-picking. The central task of ARIA is the assignment of ambiguous NOEs during the structure calculation using a combination of ambiguous distance restraints and an iterative assignment strategy. In addition, ARIA calibrates ambiguous NOEs to derive distance restraints, merges overlapping data sets to remove duplicate information, and uses empirical rules to identify erroneous peaks. While the distance restraints for the structure calculations were exclusively extracted from homonuclear 2D experiments, ARIA is especially suited for the analysis of multidimensional spectra. Applied to the pleckstrin homology domain, ARIA generated structures of good quality, and of sufficiently high accuracy to solve the X-ray crystal structure of the same domain by molecular replacement. The comparison of the free NMR solution structure to the X-ray structure, which is complexed to D-myo-inositol-1,4,5-triphosphate, shows that the ligand primarily induces a disorder-order transition in the binding loops, which are disordered in the NMR ensemble but well ordered in the crystal. The structural core of the protein is unaffected, as evidenced by a backbone root-mean-square difference between the average NMR coordinates and the X-ray crystal structure for the secondary structure elements of less than 0.6 A.

Selected figure(s)

Figure 3.
Figure 3. C^α traces of the seven lowest energy structures: a, iteration 0; b, iteration 1; c, last iteration.

Figure 8.
Figure 8. The ensemble of 50 final structures. (a) C^αtrace of all residues; (b) side-chains forming the hydrophobic core around Trp99; (c) Overlay of the 50 NMR structure (in grey) and the X-ray crystal structure [Hyvonen et al 1995]. The residues involved in IP3 binding are shown.

The above figures are reprinted by permission from Elsevier: J Mol Biol (1997, 269, 408-422) copyright 1997.

Figures were selected by an automated process.