Crystal structure of the SH3 domain of growth factor receptor-bound protein 2

Bolgov, Alexandr; Korban, Svetlana A.; Luzik, Dmitrii; Zhemkov, Vladimir; Kim, Meewhi; Rogacheva, Olga N.; Bezprozvanny, Ilya

doi:10.1107/s2053230x20007232

Cited by 6 publications

(6 citation statements)

References 36 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…This stands in sharp contrast to the nSrc-loop structure of the Grb2-nSH3 domain. Whereas the nSrc-loop is well defined and interacts with Gab1 residues R 507 PV 509 in the Grb2-Gab1 497-528 complex, it is highly variable in NMR structures of the SOS1 1149-1158 Grb2-nSH3 complex, disordered in the Grb2 dimer structure and adopts differing crystal packing influenced conformations in structures of ligand-free Grb2-nSH3 (29,(46)(47)(48) , suggesting inherent flexibility of this loop. The nSrc-loop conformation observed in the present structure resembles that of a ligand-free Grb2-nSH3 structure in which the proline-rich C-terminus of a crystallographic neighbor interacts with the S3/nSrc-loop region, suggesting that this might be a preferred conformation for peptide bound Grb2 nSH3 (Fig.…”

Section: Discussionmentioning

confidence: 99%

“…Structural superposition of the C-traces of nSH3-Grb2 in complex with Gab 497-528 , the minimized average NMR structure of the nSH3-Grb2-SOS1 1149-1158 complex (yellow) and the crystal structures of the nSH3 domain of ligand-free Grb2 (blue) and of the two molecules in the asymmetric unit of ligandfree nSH3-Grb2 (red, chain A and violet, chain B) (29,46,47). In the ligand-free nSH3-Grb2 crystal structure, the proline-containing C-termini of two neighboring nSH3 domains interact with the binding site of chain B nSH3 by mimicking S1/S2-binding and S3/nSrc-loop-binding, respectively.…”

Section: (E)mentioning

confidence: 99%

See 1 more Smart Citation

Self-assembly of Grb2 meshworks revealed by Grb2-Gab1_497-528complex structure

Breithaupt¹,

Gruber

Mandel

et al. 2023

Preprint

View full text Add to dashboard Cite

The ubiquitously expressed adaptor protein Growth factor receptor bound protein 2 (Grb2) plays an essential role in signal transduction by binding to activated receptor tyrosine kinases through its SH2 domain and to downstream effectors via its N- and C-terminal SH3 domains (nSH3, cSH3). Here we present the first structure of ligand-bound full length Grb2. The crystal structure of Grb2 in complex with a bidentate nSH3-cSH3-binding peptide, derived from the multi-site docking protein Grb2-associated binder-1 (Gab1), provides molecular insight into effector recognition by Grb2 and reveals the assembly of a two-dimensional meshwork, consisting of multimeric filament-like Grb2 chains linked to each other by the bivalent bound Gab1497-528peptide. Dominant contacts between Grb2 molecules in the multimer are provided by an intermolecular SH2/cSH3 domain interface that is also present in the closed dimer of ligand-free Grb2. We further show that Grb2 is able to self-assemble to form phase-separated condensates in solution. The Grb2 SH2 domain phosphotyrosine binding site is freely accessible in the multimeric assembly, and phase separation is fostered by addition of Gab1497-528, as expected from the crystal structure. Multimeric assembly is also observed using a Grb2 SH2-cSH3 didomain construct, and suppressed using a Grb2 Tyr60Glu mutant, a mimic of the in vivo phosphorylated Tyr160 central to the SH2/cSH3 interface, demonstrating that an intact SH2/cSH3 interface is needed for Grb2 assembly in solution.

show abstract

Section: Discussionmentioning

confidence: 99%

Section: (E)mentioning

confidence: 99%

Self-assembly of Grb2 meshworks revealed by Grb2-Gab1_497-528complex structure

Breithaupt¹,

Gruber

Mandel

et al. 2023

Preprint

View full text Add to dashboard Cite

show abstract

“…Crystallographic studies of the GRB2 n-SH3 domain have revealed its dimeric structure, with chains A and B present in the asymmetric unit. The SOS1-binding site in chain A involves specific residues, including Tyr7, Phe8, Trp36, Pro49, and Tyr52 [ 103 ]. In contrast, the SOS1 pocket in chain B is observed in a complex with the KPHPG residues from the C-terminus of chain A.…”

Section: Overview the Proteins Interacting With The Grb2 Sh3 Domainmentioning

confidence: 99%

The Configuration of GRB2 in Protein Interaction and Signal Transduction

Wang,

Liu,

Meng

et al. 2024

Biomolecules

View full text Add to dashboard Cite

Growth-factor-receptor-binding protein 2 (GRB2) is a non-enzymatic adaptor protein that plays a pivotal role in precisely regulated signaling cascades from cell surface receptors to cellular responses, including signaling transduction and gene expression. GRB2 binds to numerous target molecules, thereby modulating a complex cell signaling network with diverse functions. The structural characteristics of GRB2 are essential for its functionality, as its multiple domains and interaction mechanisms underpin its role in cellular biology. The typical signaling pathway involving GRB2 is initiated by the ligand stimulation to its receptor tyrosine kinases (RTKs). The activation of RTKs leads to the recruitment of GRB2 through its SH2 domain to the phosphorylated tyrosine residues on the receptor. GRB2, in turn, binds to the Son of Sevenless (SOS) protein through its SH3 domain. This binding facilitates the activation of Ras, a small GTPase, which triggers a cascade of downstream signaling events, ultimately leading to cell proliferation, survival, and differentiation. Further research and exploration into the structure and function of GRB2 hold great potential for providing novel insights and strategies to enhance medical approaches for related diseases. In this review, we provide an outline of the proteins that engage with domains of GRB2, along with the function of different GRB2 domains in governing cellular signaling pathways. This furnishes essential points of current studies for the forthcoming advancement of therapeutic medications aimed at GRB2.

show abstract

“…As an alternative, we employed a partially processed experimental SF file which has not been merged to high symmetry. This strategy was tested on the structure with PDB code 6sdf, for which we have the complete set of raw diffraction data (Bolgov et al, 2020).…”

Section: Using Unsymmetrized Datamentioning

confidence: 99%

Modeling a unit cell: crystallographic refinement procedure using the biomolecular MD simulation platform Amber

Mikhailovskii

Xue

Skrynnikov

2021

Int Union Crystallogr J

View full text Add to dashboard Cite

A procedure has been developed for the refinement of crystallographic protein structures based on the biomolecular simulation program Amber. The procedure constructs a model representing a crystal unit cell, which generally contains multiple protein molecules and is fully hydrated with TIP3P water. Periodic boundary conditions are applied to the cell in order to emulate the crystal lattice. The refinement is conducted in the form of a specially designed short molecular-dynamics run controlled by the Amber ff14SB force field and the maximum-likelihood potential that encodes the structure-factor-based restraints. The new Amber-based refinement procedure has been tested on a set of 84 protein structures. In most cases, the new procedure led to appreciably lower R free values compared with those reported in the original PDB depositions or obtained by means of the industry-standard phenix.refine program. In particular, the new method has the edge in refining low-accuracy scrambled models. It has also been successful in refining a number of molecular-replacement models, including one with an r.m.s.d. of 2.15 Å. In addition, Amber-refined structures consistently show superior MolProbity scores. The new approach offers a highly realistic representation of protein–protein interactions in the crystal, as well as of protein–water interactions. It also offers a realistic representation of protein crystal dynamics (akin to ensemble-refinement schemes). Importantly, the method fully utilizes the information from the available diffraction data, while relying on state-of-the-art molecular-dynamics modeling to assist with those elements of the structure that do not diffract well (for example mobile loops or side chains). Finally, it should be noted that the protocol employs no tunable parameters, and the calculations can be conducted in a matter of several hours on desktop computers equipped with graphical processing units or using a designated web service.

show abstract

Crystal structure of the SH3 domain of growth factor receptor-bound protein 2

Cited by 6 publications

References 36 publications

Self-assembly of Grb2 meshworks revealed by Grb2-Gab1_497-528complex structure

Self-assembly of Grb2 meshworks revealed by Grb2-Gab1_497-528complex structure

The Configuration of GRB2 in Protein Interaction and Signal Transduction

Modeling a unit cell: crystallographic refinement procedure using the biomolecular MD simulation platform Amber

Contact Info

Product

Resources

About

Crystal structure of the SH3 domain of growth factor receptor-bound protein 2

Cited by 6 publications

References 36 publications

Self-assembly of Grb2 meshworks revealed by Grb2-Gab1497-528complex structure

Self-assembly of Grb2 meshworks revealed by Grb2-Gab1497-528complex structure

The Configuration of GRB2 in Protein Interaction and Signal Transduction

Modeling a unit cell: crystallographic refinement procedure using the biomolecular MD simulation platform Amber

Contact Info

Product

Resources

About

Self-assembly of Grb2 meshworks revealed by Grb2-Gab1_497-528complex structure

Self-assembly of Grb2 meshworks revealed by Grb2-Gab1_497-528complex structure