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- PDB-2w0z: Grb2 SH3C (3) -

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Basic information

Entry
Database: PDB / ID: 2w0z
TitleGrb2 SH3C (3)
Components
  • GRB2-ASSOCIATED-BINDING PROTEIN 2
  • GROWTH FACTOR RECEPTOR-BOUND PROTEIN 2
KeywordsSIGNALING PROTEIN / POLYMORPHISM / PHOSPHOPROTEIN / GOLGI APPARATUS / ALTERNATIVE SPLICING / HOST-VIRUS INTERACTION / SH3C / GRB2 / SIGNALING / SH2 DOMAIN / SH3 DOMAIN
Function / homology
Function and homology information


guanyl-nucleotide exchange factor adaptor activity / Grb2-EGFR complex / positive regulation of mast cell degranulation / branching involved in labyrinthine layer morphogenesis / STAT5 Activation / Co-inhibition by BTLA / COP9 signalosome / neurotrophin TRKA receptor binding / Activated NTRK2 signals through PI3K / MET receptor recycling ...guanyl-nucleotide exchange factor adaptor activity / Grb2-EGFR complex / positive regulation of mast cell degranulation / branching involved in labyrinthine layer morphogenesis / STAT5 Activation / Co-inhibition by BTLA / COP9 signalosome / neurotrophin TRKA receptor binding / Activated NTRK2 signals through PI3K / MET receptor recycling / transmembrane receptor protein tyrosine kinase adaptor activity / phosphatidylinositol-3,4-bisphosphate binding / Signaling by cytosolic FGFR1 fusion mutants / Interleukin-15 signaling / MET activates PTPN11 / negative regulation of natural killer cell mediated cytotoxicity / MET activates RAP1 and RAC1 / vesicle membrane / Signaling by LTK / CD28 dependent Vav1 pathway / MET activates PI3K/AKT signaling / Signal regulatory protein family interactions / epidermal growth factor receptor binding / Regulation of KIT signaling / PI-3K cascade:FGFR3 / natural killer cell mediated cytotoxicity / STAT5 activation downstream of FLT3 ITD mutants / PI-3K cascade:FGFR2 / PI-3K cascade:FGFR4 / PI-3K cascade:FGFR1 / positive regulation of actin filament polymerization / endodermal cell differentiation / phosphatidylinositol-3,4,5-trisphosphate binding / GRB2:SOS provides linkage to MAPK signaling for Integrins / RHOU GTPase cycle / regulation of MAPK cascade / RET signaling / Interleukin-3, Interleukin-5 and GM-CSF signaling / PI3K Cascade / PI3K events in ERBB2 signaling / insulin receptor substrate binding / signal transduction in response to DNA damage / SOS-mediated signalling / fibroblast growth factor receptor signaling pathway / Activated NTRK3 signals through RAS / Activated NTRK2 signals through RAS / Role of LAT2/NTAL/LAB on calcium mobilization / SHC1 events in ERBB4 signaling / Interleukin receptor SHC signaling / RHO GTPases Activate WASPs and WAVEs / GAB1 signalosome / Signalling to RAS / Signal attenuation / Activated NTRK2 signals through FRS2 and FRS3 / SHC-related events triggered by IGF1R / Schwann cell development / SHC-mediated cascade:FGFR3 / MET activates RAS signaling / SHC-mediated cascade:FGFR2 / Signaling by PDGFRA transmembrane, juxtamembrane and kinase domain mutants / Signaling by PDGFRA extracellular domain mutants / SHC-mediated cascade:FGFR4 / Erythropoietin activates RAS / SHC-mediated cascade:FGFR1 / Signaling by FGFR4 in disease / ephrin receptor binding / FRS-mediated FGFR3 signaling / Signaling by CSF3 (G-CSF) / Signaling by FLT3 ITD and TKD mutants / FRS-mediated FGFR2 signaling / FRS-mediated FGFR4 signaling / FRS-mediated FGFR1 signaling / Signaling by FGFR3 in disease / Tie2 Signaling / Signaling by FGFR2 in disease / phosphotyrosine residue binding / myelination / GRB2 events in EGFR signaling / Signaling by FLT3 fusion proteins / SHC1 events in EGFR signaling / FLT3 Signaling / Signaling by FGFR1 in disease / EGFR Transactivation by Gastrin / FCERI mediated Ca+2 mobilization / NCAM signaling for neurite out-growth / Downstream signal transduction / GRB2 events in ERBB2 signaling / insulin-like growth factor receptor signaling pathway / Insulin receptor signalling cascade / SHC1 events in ERBB2 signaling / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / osteoclast differentiation / Constitutive Signaling by Overexpressed ERBB2 / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / T cell activation / InlB-mediated entry of Listeria monocytogenes into host cell / cellular response to ionizing radiation / B cell receptor signaling pathway / FCGR3A-mediated phagocytosis / Regulation of signaling by CBL
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 / SH3 type barrels. / Src homology 3 domains / 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: 1.7 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
DepositionOct 13, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 26, 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

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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)7,5702
Polymers7,5702
Non-polymers00
Water93752
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1020 Å2
ΔGint-3.9 kcal/mol
Surface area5310 Å2
MethodPQS
Unit cell
Length a, b, c (Å)47.150, 28.705, 45.114
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein GROWTH FACTOR RECEPTOR-BOUND PROTEIN 2 / 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: 958.155 Da / Num. of mol.: 1 / Fragment: SH3 BINDING REGION, RESIDUES 350-358 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: Q9UQC2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 52 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, PRO 212 TO ALA
Sequence detailsN-TERMINAL GP OVERHANG DUE TO EXPRESSION VECTOR

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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: 1.84 Å3/Da / Density % sol: 32.7 % / Description: NONE
Crystal growpH: 7.5 / Details: 0.7 M TRISODIUM CITRATE, 0.1 M TRIS PH 8.5

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.976
DetectorType: ADSC CCD / Detector: CCD / Date: Sep 12, 2008 / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.7→20 Å / Num. obs: 7072 / % possible obs: 98.8 % / Observed criterion σ(I): 1 / Redundancy: 6.7 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 38.7
Reflection shellResolution: 1.7→1.72 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 6.3 / % possible all: 84.3

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Processing

Software
NameVersionClassification
REFMAC5.5.0047refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2VDF

2vdf


Resolution: 1.7→45.13 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.941 / SU B: 2.294 / SU ML: 0.076 / Cross valid method: THROUGHOUT / ESU R: 0.123 / ESU R Free: 0.106 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.206 334 4.7 %RANDOM
Rwork0.193 ---
obs0.194 6720 98.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.47 Å2
Baniso -1Baniso -2Baniso -3
1--1.01 Å20 Å20 Å2
2---0.29 Å20 Å2
3---1.29 Å2
Refinement stepCycle: LAST / Resolution: 1.7→45.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms534 0 0 52 586
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.022559
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3341.942765
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.84567
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.28523.66730
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.1391573
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.278154
X-RAY DIFFRACTIONr_chiral_restr0.0880.271
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023471
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8941.5340
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.6592551
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.4433219
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it44.5213
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: 1.7→1.75 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.301 21
Rwork0.214 417

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