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- PDB-4gbq: SOLUTION NMR STRUCTURE OF THE GRB2 N-TERMINAL SH3 DOMAIN COMPLEXE... -

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Basic information

Entry
Database: PDB / ID: 4gbq
TitleSOLUTION 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, 15 STRUCTURES
Components
  • GRB2
  • SOS-1
KeywordsCOMPLEX (SIGNAL TRANSDUCTION/PEPTIDE) / COMPLEX (SIGNAL TRANSDUCTION-PEPTIDE) / SH3 DOMAIN / COMPLEX (SIGNAL TRANSDUCTION-PEPTIDE) complex
Function / homology
Function and homology information


Signalling to RAS / Activated NTRK2 signals through FRS2 and FRS3 / SHC1 events in ERBB4 signaling / GRB2 events in ERBB2 signaling / EGFR Transactivation by Gastrin / SHC-mediated cascade:FGFR3 / SHC-mediated cascade:FGFR4 / SHC-mediated cascade:FGFR1 / SHC-mediated cascade:FGFR2 / MET activates PI3K/AKT signaling ...Signalling to RAS / Activated NTRK2 signals through FRS2 and FRS3 / SHC1 events in ERBB4 signaling / GRB2 events in ERBB2 signaling / EGFR Transactivation by Gastrin / SHC-mediated cascade:FGFR3 / SHC-mediated cascade:FGFR4 / SHC-mediated cascade:FGFR1 / SHC-mediated cascade:FGFR2 / MET activates PI3K/AKT signaling / PI-3K cascade:FGFR3 / PI-3K cascade:FGFR4 / SHC-related events triggered by IGF1R / Signal regulatory protein family interactions / PI-3K cascade:FGFR1 / PI-3K cascade:FGFR2 / SOS-mediated signalling / FRS-mediated FGFR3 signaling / FRS-mediated FGFR4 signaling / MET activates RAS signaling / MET activates PTPN11 / Costimulation by the CD28 family / FRS-mediated FGFR1 signaling / FRS-mediated FGFR2 signaling / PI3K events in ERBB2 signaling / Tie2 Signaling / GRB2 events in EGFR signaling / SHC1 events in EGFR signaling / Interleukin-15 signaling / FLT3 Signaling / CD28 dependent Vav1 pathway / MET activates RAP1 and RAC1 / RHOU GTPase cycle / Signaling by CSF3 (G-CSF) / MET receptor recycling / NCAM signaling for neurite out-growth / Erythropoietin activates RAS / Regulation of KIT signaling / GAB1 signalosome / Role of LAT2/NTAL/LAB on calcium mobilization / PI3K Cascade / Negative regulation of FGFR3 signaling / Negative regulation of FGFR4 signaling / anatomical structure formation involved in morphogenesis / Downstream signal transduction / Negative regulation of FGFR1 signaling / Negative regulation of FGFR2 signaling / Spry regulation of FGF signaling / Insulin receptor signalling cascade / FCERI mediated MAPK activation / Negative regulation of MET activity / lymphocyte homeostasis / Signal attenuation / RHO GTPases Activate WASPs and WAVEs / NRAGE signals death through JNK / Signaling by SCF-KIT / EGFR downregulation / RAC1 GTPase cycle / GRB2:SOS provides linkage to MAPK signaling for Integrins / guanyl-nucleotide exchange factor adaptor activity / FCERI mediated Ca+2 mobilization / Grb2-EGFR complex / RAF/MAP kinase cascade / Interleukin receptor SHC signaling / G alpha (12/13) signalling events / midbrain morphogenesis / PIP3 activates AKT signaling / regulation of pro-B cell differentiation / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / Regulation of signaling by CBL / vitellogenesis / Regulation of actin dynamics for phagocytic cup formation / pericardium morphogenesis / cardiac atrium morphogenesis / Cargo recognition for clathrin-mediated endocytosis / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / branching involved in labyrinthine layer morphogenesis / Clathrin-mediated endocytosis / RET signaling / heart trabecula morphogenesis / COP9 signalosome / vesicle membrane / neurotrophin TRKA receptor binding / regulation of T cell differentiation in thymus / transmembrane receptor protein tyrosine kinase adaptor activity / GTPase complex / positive regulation of small GTPase mediated signal transduction / positive regulation of Ras protein signal transduction / blood vessel morphogenesis / DAP12 signaling / positive regulation of epidermal growth factor receptor signaling pathway / epidermal growth factor receptor binding / small GTPase-mediated signal transduction / positive regulation of actin filament polymerization / regulation of T cell proliferation / endodermal cell differentiation / roof of mouth development / ERBB2-ERBB3 signaling pathway / eyelid development in camera-type eye / regulation of MAPK cascade
Similarity search - Function
GRB2, N-terminal SH3 domain / GRB2, C-terminal SH3 domain / Grb2-like / Ras guanine-nucleotide exchange factor, conserved site / Ras Guanine-nucleotide exchange factors domain signature. / RasGEF N-terminal motif / Guanine nucleotide exchange factor for Ras-like GTPases; N-terminal motif / Ras-like guanine nucleotide exchange factor, N-terminal / Ras guanine-nucleotide exchange factors N-terminal domain profile. / Ras-like guanine nucleotide exchange factor ...GRB2, N-terminal SH3 domain / GRB2, C-terminal SH3 domain / Grb2-like / Ras guanine-nucleotide exchange factor, conserved site / Ras Guanine-nucleotide exchange factors domain signature. / RasGEF N-terminal motif / Guanine nucleotide exchange factor for Ras-like GTPases; N-terminal motif / Ras-like guanine nucleotide exchange factor, N-terminal / Ras guanine-nucleotide exchange factors N-terminal domain profile. / Ras-like guanine nucleotide exchange factor / Ras guanine-nucleotide exchange factor, catalytic domain superfamily / Ras guanine nucleotide exchange factor domain superfamily / RasGEF domain / Ras guanine-nucleotide exchange factors catalytic domain profile. / Guanine nucleotide exchange factor for Ras-like small GTPases / Ras guanine-nucleotide exchange factors catalytic domain / Dbl homology (DH) domain superfamily / RhoGEF domain / Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases / Dbl homology (DH) domain / Dbl homology (DH) domain profile. / SH3 Domains / PH domain / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / Src homology 3 domains / SH2 domain / SH3 type barrels. / SH2 domain superfamily / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Histone-fold / PH-like domain superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
Growth factor receptor-bound protein 2 / Son of sevenless homolog 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / DG, SA
AuthorsWittekind, M. / Mapelli, C. / Lee, V. / Goldfarb, V. / Friedrichs, M.S. / Meyers, C.A. / Mueller, L.
Citation
Journal: J.Mol.Biol. / Year: 1997
Title: 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.
Authors: Wittekind, M. / Mapelli, C. / Lee, V. / Goldfarb, V. / Friedrichs, M.S. / Meyers, C.A. / Mueller, L.
#1: Journal: Biochemistry / Year: 1994
Title: Orientation of Peptide Fragments from SOS Proteins Bound to the N-Terminal SH3 Domain of Grb2 Determined by NMR Spectroscopy
Authors: Wittekind, M. / Mapelli, C. / Farmer II, B.T. / Suen, K.L. / Goldfarb, V. / Tsao, J. / Lavoie, T. / Barbacid, M. / Meyers, C.A. / Mueller, L.
#2: Journal: Mol.Cell.Biol. / Year: 1993
Title: Molecular Cloning of the Mouse Grb2 Gene: Differential Interaction of the Grb2 Adaptor Protein with Epidermal Growth Factor and Nerve Growth Factor Receptors
Authors: Suen, K.L. / Bustelo, X.R. / Pawson, T. / Barbacid, M.
#3: Journal: Proc.Natl.Acad.Sci.USA / Year: 1992
Title: Identification of Murine Homologues of the Drosophila Son of Sevenless Gene: Potential Activators of Ras
Authors: Bowtell, D. / Fu, P. / Simon, M. / Senior, P.
History
DepositionDec 23, 1996Processing site: BNL
Revision 1.0Sep 4, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 16, 2022Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GRB2
B: SOS-1


Theoretical massNumber of molelcules
Total (without water)9,6522
Polymers9,6522
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)15 / 200
Representative

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Components

#1: Protein GRB2 /


Mass: 8454.495 Da / Num. of mol.: 1 / Fragment: N-TERMINAL SH3 DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Strain: BALB/C / Cell line: BL21 / Cellular location: CYTOPLASMICCytoplasm / Gene: POTENTIAL / Plasmid: BL21 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: Q60631
#2: Protein/peptide SOS-1 / AC-VPPPVPPRRR-NH2


Mass: 1197.478 Da / Num. of mol.: 1 / Fragment: RESIDUES 1135 - 1144
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cellular location: CYTOPLASM / References: UniProt: Q62245

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentType: SEE JOURNAL ARTICLE

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Sample preparation

Sample conditionspH: 6.0 / Temperature: 298. K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Varian UNITYPLUS / Manufacturer: Varian / Model: UNITYPLUS / Field strength: 600 MHz

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
NMR software
NameDeveloperClassification
X-PLORBRUNGERrefinement
X-PLORstructure solution
RefinementMethod: DG, SA / Software ordinal: 1
Details: TWO ENSEMBLES WERE CALCULATED. BOTH USED THE SAME SET OF NOE/ANGLE/J-COUPLING RESTRAINTS, BUT THEY DIFFER IN THAT THE ENSEMBLE ALSO OF THIS ENTRY AND ENTRY 4GBQ INCLUDED 1H AND 13C CHEMICAL ...Details: TWO ENSEMBLES WERE CALCULATED. BOTH USED THE SAME SET OF NOE/ANGLE/J-COUPLING RESTRAINTS, BUT THEY DIFFER IN THAT THE ENSEMBLE ALSO OF THIS ENTRY AND ENTRY 4GBQ INCLUDED 1H AND 13C CHEMICAL SHIFTS AS RESTRAINTS RMSD BOND DISTANCES 0.011 +/- 0.002 ANGSTROMS RMSD BOND ANGLE 2.90 +/- 0.19 DEGREES BACKBONE RMSD (N, CA, C, O) = 0.26 +/- 0.09 (SH3 DOMAIN RESIDUES 1 - 26, 36 - 54 AND SOS-E PEPTIDE RESIDUES 2 - 7)
NMR ensembleConformers calculated total number: 200 / Conformers submitted total number: 15

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