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- PDB-1aze: NMR STRUCTURE OF THE COMPLEX BETWEEN THE C32S-Y7V MUTANT OF THE N... -

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Basic information

Entry
Database: PDB / ID: 1aze
TitleNMR STRUCTURE OF THE COMPLEX BETWEEN THE C32S-Y7V MUTANT OF THE NSH3 DOMAIN OF GRB2 WITH A PEPTIDE FROM SOS, 10 STRUCTURES
Components
  • GRB2
  • SOS
KeywordsCOMPLEX (ADAPTOR PROTEIN/PEPTIDE) / COMPLEX (ADAPTOR PROTEIN-PEPTIDE) / SH3 DOMAIN / GUANINE-NUCLEOTIDE RELEASING FACTOR / COMPLEX (ADAPTOR PROTEIN-PEPTIDE) complex
Function / homology
Function and homology information


G alpha (12/13) signalling events / NRAGE signals death through JNK / photoreceptor cell fate determination / SOS-mediated signalling / Signaling by SCF-KIT / Regulation of KIT signaling / Signalling to RAS / Downstream signal transduction / DAP12 signaling / SHC-related events triggered by IGF1R ...G alpha (12/13) signalling events / NRAGE signals death through JNK / photoreceptor cell fate determination / SOS-mediated signalling / Signaling by SCF-KIT / Regulation of KIT signaling / Signalling to RAS / Downstream signal transduction / DAP12 signaling / SHC-related events triggered by IGF1R / Role of LAT2/NTAL/LAB on calcium mobilization / FCERI mediated Ca+2 mobilization / SHC-mediated cascade:FGFR1 / FRS-mediated FGFR1 signaling / SHC-mediated cascade:FGFR2 / FRS-mediated FGFR2 signaling / SHC-mediated cascade:FGFR3 / FRS-mediated FGFR3 signaling / FRS-mediated FGFR4 signaling / SHC-mediated cascade:FGFR4 / Signal attenuation / Insulin receptor signalling cascade / RET signaling / FLT3 Signaling / rhabdomere microvillus membrane / FCERI mediated MAPK activation / RAC1 GTPase cycle / SHC1 events in ERBB4 signaling / GRB2 events in EGFR signaling / SHC1 events in EGFR signaling / GRB2 events in ERBB2 signaling / EGFR Transactivation by Gastrin / torso signaling pathway / NCAM signaling for neurite out-growth / tracheal outgrowth, open tracheal system / RAF/MAP kinase cascade / epithelial cell migration, open tracheal system / imaginal disc-derived leg morphogenesis / R7 cell fate commitment / sevenless signaling pathway / guanyl-nucleotide exchange factor adaptor activity / Grb2-EGFR complex / branching involved in labyrinthine layer morphogenesis / STAT5 Activation / Co-inhibition by BTLA / neurotrophin TRKA receptor binding / COP9 signalosome / Activated NTRK2 signals through PI3K / MET receptor recycling / transmembrane receptor protein tyrosine kinase adaptor activity / Signaling by cytosolic FGFR1 fusion mutants / Interleukin-15 signaling / negative regulation of natural killer cell mediated cytotoxicity / MET activates PTPN11 / MET activates RAP1 and RAC1 / positive regulation of Ras protein signal transduction / axon midline choice point recognition / vesicle membrane / Signaling by LTK / CD28 dependent Vav1 pathway / MET activates PI3K/AKT signaling / Signal regulatory protein family interactions / epidermal growth factor receptor binding / extrinsic component of cytoplasmic side of plasma membrane / Regulation of KIT signaling / PI-3K cascade:FGFR3 / natural killer cell mediated cytotoxicity / STAT5 activation downstream of FLT3 ITD mutants / PI-3K cascade:FGFR2 / negative regulation of G1/S transition of mitotic cell cycle / PI-3K cascade:FGFR4 / PI-3K cascade:FGFR1 / endodermal cell differentiation / positive regulation of actin filament polymerization / GRB2:SOS provides linkage to MAPK signaling for Integrins / RHOU GTPase cycle / regulation of MAPK cascade / positive regulation of Rac protein signal transduction / RET signaling / insulin receptor substrate binding / PI3K events in ERBB2 signaling / Interleukin-3, Interleukin-5 and GM-CSF signaling / PI3K Cascade / signal transduction in response to DNA damage / SOS-mediated signalling / fibroblast growth factor receptor signaling pathway / Activated NTRK3 signals through RAS / Role of LAT2/NTAL/LAB on calcium mobilization / Activated NTRK2 signals through RAS / positive regulation of cell size / Interleukin receptor SHC signaling / SHC1 events in ERBB4 signaling / RHO GTPases Activate WASPs and WAVEs / vascular endothelial growth factor receptor signaling pathway / Signal attenuation / Signalling to RAS / GAB1 signalosome / SHC-related events triggered by IGF1R / Activated NTRK2 signals through FRS2 and FRS3 / Schwann cell development
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-like guanine nucleotide exchange factor / Ras guanine-nucleotide exchange factors N-terminal domain profile. ...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-like guanine nucleotide exchange factor / Ras guanine-nucleotide exchange factors N-terminal domain profile. / Ras guanine nucleotide exchange factor domain superfamily / Ras guanine-nucleotide exchange factor, catalytic 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 / SH3 type barrels. / SH2 domain / Src homology 3 domains / 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
Protein son of sevenless / Growth factor receptor-bound protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
Drosophila melanogaster (fruit fly)
MethodSOLUTION NMR / SIMULATED ANNEALING ENERGY MINIMIZATION
AuthorsVidal, M. / Gincel, E. / Goudreau, N. / Cornille, F. / Parker, F. / Duchesne, M. / Tocque, B. / Garbay, C. / Roques, B.P.
Citation
Journal: J.Mol.Biol. / Year: 1999
Title: Molecular and cellular analysis of Grb2 SH3 domain mutants: interaction with Sos and dynamin.
Authors: Vidal, M. / Goudreau, N. / Cornille, F. / Cussac, D. / Gincel, E. / Garbay, C.
#1: Journal: Nat.Struct.Biol. / Year: 1994
Title: NMR Structure of the N-Terminal SH3 Domain of Grb2 and its Complex with a Proline-Rich Peptide from SOS
Authors: Goudreau, N. / Cornille, F. / Duchesne, M. / Parker, F. / Tocque, B. / Garbay, C. / Roques, B.P.
History
DepositionNov 17, 1997Processing site: BNL
Revision 1.0May 18, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GRB2
B: SOS


Theoretical massNumber of molelcules
Total (without water)7,6512
Polymers7,6512
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 50BEST ENERGY, LEAST RESTRAINT VIOLATION
Representative

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Components

#1: Protein GRB2 / ASH / GROWTH FACTOR RECEPTOR-BOUND PROTEIN 2


Mass: 6477.309 Da / Num. of mol.: 1 / Fragment: N-TERMINAL SH3 DOMAIN, RESIDUES 1 - 55 / Mutation: Y7V, C32S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GRB2 / Organ: FRUIT / References: UniProt: P62993
#2: Protein/peptide SOS


Mass: 1173.432 Da / Num. of mol.: 1 / Fragment: BINDING SITE IN H-SOS, PEPTIDE VPPPVPPRRR
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / References: UniProt: P26675

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111NOESY
121TOCSY
131COSY

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Sample preparation

DetailsContents: H2O, PHOSPHATE BUFFER 20MM, NACL 100MM
Sample conditionsIonic strength: NACL 100mM / pH: 6 / Pressure: 1 atm / Temperature: 293 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Bruker AMX600 / Manufacturer: Bruker / Model: AMX600 / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
Discover2.95BIOSYMrefinement
BRUKER UXNMR + DISCOVERDISCOVERstructure solution
RefinementMethod: SIMULATED ANNEALING ENERGY MINIMIZATION / Software ordinal: 1
NMR ensembleConformer selection criteria: BEST ENERGY, LEAST RESTRAINT VIOLATION
Conformers calculated total number: 50 / Conformers submitted total number: 10
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS

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