6SDF | pdb_00006sdf

N-terminal SH3 domain of Grb2 protein

• PDB DOI: https://doi.org/10.2210/pdb6SDF/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2019-07-26 Released: 2020-01-29 
• Deposition Author(s): Bolgov, A.A., Korban, S.A., Luzik, D.A., Rogacheva, O.N., Zhemkov, V.A., Kim, M., Skrynnikov, N.R., Bezprozvanny, I.B.
• Funding Organization(s): Russian Science Foundation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.210 (Depositor), 0.208 (DCC) 
• R-Value Work: 
  0.160 (Depositor), 0.156 (DCC) 
• R-Value Observed: 
  0.162 (Depositor) 

Starting Model: experimental

Literature

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

Bolgov, A., Korban, S., Luzik, D., Zhemkov, V., Kim, M., Rogacheva, O., Bezprozvanny, I.

(2020) Acta Crystallogr F Struct Biol Commun 76: 263-270

• PubMed: 32510467 
• DOI: https://doi.org/10.1107/S2053230X20007232
• Primary Citation Related Structures: 
  6SDF


• PubMed Abstract: 
  

  This study presents the crystal structure of the N-terminal SH3 (SH3N) domain of growth factor receptor-bound protein 2 (Grb2) at 2.5 Å resolution. Grb2 is a small (215-amino-acid) adaptor protein that is widely expressed and involved in signal transduction/cell communication. The crystal structure of full-length Grb2 has previously been reported (PDB entry 1gri). The structure of the isolated SH3N domain is consistent with the full-length structure. The structure of the isolated SH3N domain was solved at a higher resolution (2.5 Å compared with 3.1 Å for the previously deposited structure) and made it possible to resolve some of the loops that were missing in the full-length structure. In addition, interactions between the carboxy-terminal region of the SH3N domain and the Sos1-binding sites were observed in the structure of the isolated domain. Analysis of these interactions provided new information about the ligand-binding properties of the SH3N domain of Grb2.

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Organizational Affiliation: 
• Laboratory of Molecular Neurodegeneration, Institute of Biomedical systems and Biotechnologies, Peter the Great St Petersburg Polytechnic University, St Petersburg 194021, Russian Federation.
Laboratory of Biomolecular NMR, St Petersburg State University, St Petersburg 199034, Russian Federation.
Department of Physiology, UT Southwestern Medical Center at Dallas, Dallas, TX 75390, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 14.7 kDa 
• Atom Count: 1,088 
• Modeled Residue Count: 119 
• Deposited Residue Count: 122 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Growth factor receptor-bound protein 2	A, B	61	Homo sapiens	Mutation(s): 0  Gene Names: GRB2, ASH
UniProt & NIH Common Fund Data Resources
Find proteins for P62993 (Homo sapiens) Explore P62993  Go to UniProtKB:  P62993
PHAROS:  P62993 GTEx:  ENSG00000177885

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MPD	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], J [auth B]	(4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N
CL	H [auth A], I [auth A], K [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.210 (Depositor), 0.208 (DCC) 
• R-Value Work:  0.160 (Depositor), 0.156 (DCC) 
• R-Value Observed: 0.162 (Depositor) 

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 97.731	α = 90
b = 97.731	β = 90
c = 51.032	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
CrysalisPro	data reduction
CrysalisPro	data scaling
MOLREP	phasing
Coot	model building

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2020-01-29 
Deposition Author(s): Bolgov, A.A., Korban, S.A., Luzik, D.A., Rogacheva, O.N., Zhemkov, V.A., Kim, M., Skrynnikov, N.R., Bezprozvanny, I.B.

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Funding Organization	Location	Grant Number
Russian Science Foundation	Russian Federation	19-15-00184

Revision History  

• Version 1.0: 2020-01-29
  Type: Initial release
  
• Version 1.1: 2020-07-08
  Changes: Database references
• Version 1.2: 2024-01-24
  Changes: Advisory, Data collection, Database references, Refinement description