PDBsum entry 3gbq

Complex (signal transduction/peptide)

PDB id: 3gbq

Contents

Protein chains

57 a.a. *

12 a.a. *

* Residue conservation analysis

PDB id:

3gbq

Name:

Complex (signal transduction/peptide)

Title:

Solution nmr structure of the grb2 n-terminal sh3 domain complexed with a ten-residue peptide derived from sos direct refinement against noes, j-couplings, and 1h and 13c chemical shifts, minimized average structure

Structure:

Grb2. Chain: a. Fragment: n-terminal sh3 domain. Engineered: yes. Sos-1. Chain: b. Fragment: residues 1135 - 1144. Synonym: ac-vpppvpprrr-nh2. Engineered: yes

Source:

Mus musculus. House mouse. Organism_taxid: 10090. Strain: balb/c. Cell_line: bl21. Cellular_location: cytoplasmic. Gene: potential. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

NMR struc:

1 models

Authors:

M.Wittekind,C.Mapelli,V.Lee,V.Goldfarb,M.S.Friedrichs,C.A.Meyers, L.Mueller

Key ref:

M.Wittekind et al. (1997). Solution structure of the Grb2 N-terminal SH3 domain complexed with a ten-residue peptide derived from SOS: direct refinement against NOEs, J-couplings and 1H and 13C chemical shifts. J Mol Biol, 267, 933-952. PubMed id: 9135122 DOI: 10.1006/jmbi.1996.0886

Date:

23-Dec-96 Release date: 04-Sep-97

Protein chain

Q60631  (GRB2_MOUSE) -  Growth factor receptor-bound protein 2 from Mus musculus

Seq: 217 a.a.

Struc: 57 a.a.

Protein chain

Q62245  (SOS1_MOUSE) -  Son of sevenless homolog 1 from Mus musculus

Seq: 1319 a.a.

Struc: 11 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

DOI no: 10.1006/jmbi.1996.0886

J Mol Biol 267:933-952 (1997)

PubMed id: 9135122

Solution structure of the Grb2 N-terminal SH3 domain complexed with a ten-residue peptide derived from SOS: direct refinement against NOEs, J-couplings and 1H and 13C chemical shifts.

M.Wittekind, C.Mapelli, V.Lee, V.Goldfarb, M.S.Friedrichs, C.A.Meyers, L.Mueller.

ABSTRACT

Refined ensembles of solution structures have been calculated for the N-terminal SH3 domain of Grb2 (N-SH3) complexed with the ac-VPPPVPPRRR-nh2 peptide derived from residues 1135 to 1144 of the mouse SOS-1 sequence. NMR spectra obtained from different combinations of both 13C-15N-labeled and unlabeled N-SH3 and SOS peptide fragment were used to obtain stereo-assignments for pro-chiral groups of the peptide, angle restraints via heteronuclear coupling constants, and complete 1H, 13C, and 15N resonance assignments for both molecules. One ensemble of structures was calculated using conventional methods while a second ensemble was generated by including additional direct refinements against both 1H and 13C(alpha)/13C(beta) chemical shifts. In both ensembles, the protein:peptide interface is highly resolved, reflecting the inclusion of 110 inter-molecular nuclear Overhauser enhancement (NOE) distance restraints. The first and second peptide-binding sub-sites of N-SH3 interact with structurally well-defined portions of the peptide. These interactions include hydrogen bonds and extensive hydrophobic contacts. In the third highly acidic sub-site, the conformation of the peptide Arg8 side-chain is partially ordered by a set of NOE restraints to the Trp36 ring protons. Overall, several lines of evidence point to dynamical averaging of peptide and N-SH3 side-chain conformations in the third subsite. These conformations are characterized by transient charge stabilized hydrogen bond interactions between the peptide arginine side-chain hydrogen bond donors and either single, or possibly multiple, acceptor(s) in the third peptide-binding sub-site.

Selected figure(s)

Figure 6.
Figure 6. Phi/Psi plots for N-SH3 and the SOS-E pep- tide in the minimized average hSA CS i N-SH3:SOS-E complex structure. Glycine residues are denoted by x and non-glycines with &. A, Phi and psi angle values are plotted for N-SH3 residues 1 to 26, 36 to 55. The dis- ordered loop comprised of N-SH3 residues 27 to 35 is omitted for clarity. B, Similar plot of SOS-E residues 1 to 10.

Figure 8.
Figure 8. Stereo view of the back- bone atoms of N-SH3 residues Ala5 to Asp23 and Lys50 to Ile53. The Figure shows the SH3 conserved ``AXD'' sequence (Ala5 to Phe9), the variable RT-loop (resi- dues Lys10 to Ser18) including the 3 10 helix-like turn at Ala13 to Glu16, the type II turn at the SH3 conserved ``RGD'' loop (Arg21 to Asp23), and the conserved 310 helix (Lys50 to Ile53). Backbone (N, C a , C) atoms (gray); HN (light blue, unprotected from solvent exchange; blue, protected from solvent exchange); O (pink, non-H-bond acceptor; red, H-bond acceptor); side-chain carbon atoms (white); side-chain oxygen atoms (magenta). The side-chains of residues that participate in H-bonds (Asp8, Ser18, and Asp23) are shown (see the text). H-bonds are depicted as colored broken lines: included in the structure calculations as restraints (green); not included as restraints but amide proton donor protected from solvent exchange and H-bond observed in at least 75% of the chemical shift refined structures (yel- low); same as yellow but amide proton donor not protected from solvent exchange (white). This Figure was made with the program INSIGHTII (Molecular Simulations, San Diego CA).

The above figures are reprinted by permission from Elsevier: J Mol Biol (1997, 267, 933-952) copyright 1997.

Figures were selected by an automated process.