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- PDB-2vwf: Grb2 SH3C (2) -

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Basic information

Entry
Database: PDB / ID: 2vwf
TitleGrb2 SH3C (2)
Components
  • GRB2-ASSOCIATED-BINDING PROTEIN 2
  • GROWTH FACTOR RECEPTOR-BOUND PROTEIN 2GRB2
KeywordsPROTEIN BINDING / POLYMORPHISM / PHOSPHOPROTEIN / GOLGI APPARATUS / GRB2 / ALTERNATIVE SPLICING / HOST-VIRUS INTERACTION / SH3C / SIGNALING / SH2 DOMAIN / SH3 DOMAIN / PROTEIN-BINDING
Function / homology
Function and homology information


guanyl-nucleotide exchange factor adaptor activity / Grb2-EGFR complex / branching involved in labyrinthine layer morphogenesis / positive regulation of mast cell degranulation / STAT5 Activation / COP9 signalosome / vesicle membrane / neurotrophin TRKA receptor binding / Activated NTRK2 signals through PI3K / phosphatidylinositol-3,4-bisphosphate binding ...guanyl-nucleotide exchange factor adaptor activity / Grb2-EGFR complex / branching involved in labyrinthine layer morphogenesis / positive regulation of mast cell degranulation / STAT5 Activation / COP9 signalosome / vesicle membrane / neurotrophin TRKA receptor binding / Activated NTRK2 signals through PI3K / phosphatidylinositol-3,4-bisphosphate binding / MET receptor recycling / transmembrane receptor protein tyrosine kinase adaptor activity / Signaling by cytosolic FGFR1 fusion mutants / Interleukin-15 signaling / MET activates PTPN11 / MET activates RAP1 and RAC1 / CD28 dependent Vav1 pathway / Costimulation by the CD28 family / MET activates PI3K/AKT signaling / Signal regulatory protein family interactions / Regulation of KIT signaling / epidermal growth factor receptor binding / positive regulation of actin filament polymerization / PI-3K cascade:FGFR3 / STAT5 activation downstream of FLT3 ITD mutants / PI-3K cascade:FGFR2 / PI-3K cascade:FGFR4 / PI-3K cascade:FGFR1 / endodermal cell differentiation / phosphatidylinositol-3,4,5-trisphosphate binding / regulation of MAPK cascade / GRB2:SOS provides linkage to MAPK signaling for Integrins / RHOU GTPase cycle / PI3K events in ERBB2 signaling / Signaling by ALK fusions and activated point mutants / SOS-mediated signalling / Activated NTRK3 signals through RAS / RET signaling / Activated NTRK2 signals through RAS / insulin receptor substrate binding / PI3K Cascade / Interleukin-3, Interleukin-5 and GM-CSF signaling / SHC1 events in ERBB4 signaling / RHO GTPases Activate WASPs and WAVEs / Signalling to RAS / fibroblast growth factor receptor signaling pathway / GAB1 signalosome / SHC-related events triggered by IGF1R / Activated NTRK2 signals through FRS2 and FRS3 / Role of LAT2/NTAL/LAB on calcium mobilization / Signal attenuation / Interleukin receptor SHC signaling / SHC-mediated cascade:FGFR3 / MET activates RAS signaling / Schwann cell development / Signaling by PDGFRA transmembrane, juxtamembrane and kinase domain mutants / Signaling by PDGFRA extracellular domain mutants / SHC-mediated cascade:FGFR2 / SHC-mediated cascade:FGFR4 / Signaling by FGFR4 in disease / SHC-mediated cascade:FGFR1 / Erythropoietin activates RAS / signal transduction in response to DNA damage / FRS-mediated FGFR3 signaling / Signaling by CSF3 (G-CSF) / Signaling by FLT3 ITD and TKD mutants / FRS-mediated FGFR2 signaling / FRS-mediated FGFR4 signaling / Signaling by FGFR3 in disease / FRS-mediated FGFR1 signaling / Tie2 Signaling / Signaling by FGFR2 in disease / GRB2 events in EGFR signaling / SHC1 events in EGFR signaling / myelination / EGFR Transactivation by Gastrin / Signaling by FLT3 fusion proteins / FLT3 Signaling / Signaling by FGFR1 in disease / GRB2 events in ERBB2 signaling / NCAM signaling for neurite out-growth / phosphotyrosine residue binding / ephrin receptor binding / SHC1 events in ERBB2 signaling / Downstream signal transduction / Insulin receptor signalling cascade / Constitutive Signaling by Overexpressed ERBB2 / FCERI mediated Ca+2 mobilization / osteoclast differentiation / InlB-mediated entry of Listeria monocytogenes into host cell / insulin-like growth factor receptor signaling pathway / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / phosphatidylinositol 3-kinase/protein kinase B signal transduction / cellular response to ionizing radiation / Regulation of signaling by CBL / Negative regulation of FGFR3 signaling / Negative regulation of FGFR2 signaling / FCGR3A-mediated phagocytosis / FCERI mediated MAPK activation
Similarity search - Function
GRB2-associated-binding protein 1-4-like / GRB2, N-terminal SH3 domain / GRB2, C-terminal SH3 domain / Grb2-like / SH3 Domains / PH domain / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / SH3 domain ...GRB2-associated-binding protein 1-4-like / GRB2, N-terminal SH3 domain / GRB2, C-terminal SH3 domain / Grb2-like / 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 / SH2 domain / Src homology 3 domains / SH3 type barrels. / SH2 domain superfamily / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / PH-like domain superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
Growth factor receptor-bound protein 2 / GRB2-associated-binding protein 2
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.58 Å
AuthorsHarkiolaki, M. / Tsirka, T. / Feller, S.M.
CitationJournal: Structure / Year: 2009
Title: Distinct Binding Modes of Two Epitopes in Gab2 that Interact with the Sh3C Domain of Grb2.
Authors: Harkiolaki, M. / Tsirka, T. / Lewitzky, M. / Simister, P.C. / Joshi, D. / Bird, L.E. / Jones, E.Y. / O'Reilly, N. / Feller, S.M.
History
DepositionJun 24, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 19, 2009Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GROWTH FACTOR RECEPTOR-BOUND PROTEIN 2
B: GRB2-ASSOCIATED-BINDING PROTEIN 2


Theoretical massNumber of molelcules
Total (without water)8,3882
Polymers8,3882
Non-polymers00
Water75742
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1370 Å2
ΔGint-8.2 kcal/mol
Surface area5450 Å2
MethodPQS
Unit cell
Length a, b, c (Å)41.166, 41.166, 107.915
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-2020-

HOH

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Components

#1: Protein GROWTH FACTOR RECEPTOR-BOUND PROTEIN 2 / GRB2 / ADAPTER PROTEIN GRB2 / SH2/SH3 ADAPTER GRB2 / PROTEIN ASH / GRB2 SH3C


Mass: 6612.233 Da / Num. of mol.: 1 / Fragment: SH3 DOMAIN, RESIDUES 159-214 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: N-TERMINAL GP- OVERHANG DUE TO INFUSION VECTOR USED
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: OPIN J / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P62993
#2: Protein/peptide GRB2-ASSOCIATED-BINDING PROTEIN 2 / GROWTH FACTOR RECEPTOR BOUND PROTEIN 2-ASSOCIATED PROTEIN 2 / GRB2-ASSOCIATED BINDER 2 / PP100 / GAB2


Mass: 1776.090 Da / Num. of mol.: 1 / Fragment: SH3 BINDING REGION, RESIDUES 508-522 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: Q9UQC2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 42 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, PRO 212 TO ALA
Sequence detailsN-TERMINAL GP SEQUENCE IS DUE TO THE VECTOR USED.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.58 Å3/Da / Density % sol: 22.1 % / Description: NONE
Crystal growpH: 7
Details: 2M TRI-AMMONIUM CITRATE, 0.1M BIS-TRIS PROPANE PH7, pH 7.0

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.9537
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 8, 2007 / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.58→50 Å / Num. obs: 8066 / % possible obs: 99.9 % / Observed criterion σ(I): 1 / Redundancy: 19.5 % / Rmerge(I) obs: 0.01 / Net I/σ(I): 26.7
Reflection shellResolution: 1.58→1.64 Å / Redundancy: 19.3 % / Rmerge(I) obs: 1 / Mean I/σ(I) obs: 2.3 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2VVK

2vvk


Resolution: 1.58→35.65 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.946 / SU B: 1.814 / SU ML: 0.065 / Cross valid method: THROUGHOUT / ESU R: 0.104 / ESU R Free: 0.1 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.21907 369 4.6 %RANDOM
Rwork0.18812 ---
obs0.18951 7645 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.39 Å2
Baniso -1Baniso -2Baniso -3
1-0.54 Å20.27 Å20 Å2
2--0.54 Å20 Å2
3----0.82 Å2
Refinement stepCycle: LAST / Resolution: 1.58→35.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms570 0 0 42 612
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.022592
X-RAY DIFFRACTIONr_bond_other_d0.0070.02409
X-RAY DIFFRACTIONr_angle_refined_deg1.5971.922806
X-RAY DIFFRACTIONr_angle_other_deg0.9673985
X-RAY DIFFRACTIONr_dihedral_angle_1_deg17.584570
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.7392435
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.1711586
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.963155
X-RAY DIFFRACTIONr_chiral_restr0.0960.278
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02674
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02129
X-RAY DIFFRACTIONr_nbd_refined0.1980.294
X-RAY DIFFRACTIONr_nbd_other0.2110.2411
X-RAY DIFFRACTIONr_nbtor_refined0.1890.2285
X-RAY DIFFRACTIONr_nbtor_other0.0920.2320
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1180.225
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2550.210
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2680.236
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0820.26
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2941.5443
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.5312570
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.3613282
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.3614.5235
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.58→1.621 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.256 25
Rwork0.253 543

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