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- PDB-6sdf: N-terminal SH3 domain of Grb2 protein -

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Basic information

Entry
Database: PDB / ID: 6sdf
TitleN-terminal SH3 domain of Grb2 protein
ComponentsGrowth factor receptor-bound protein 2
KeywordsSIGNALING PROTEIN / growth factor / Grb2 / SH3-domain
Function / homology
Function and homology information


guanyl-nucleotide exchange factor adaptor activity / Grb2-EGFR complex / branching involved in labyrinthine layer morphogenesis / STAT5 Activation / Co-inhibition by BTLA / COP9 signalosome / neurotrophin TRKA receptor binding / Activated NTRK2 signals through PI3K / transmembrane receptor protein tyrosine kinase adaptor activity / MET receptor recycling ...guanyl-nucleotide exchange factor adaptor activity / Grb2-EGFR complex / branching involved in labyrinthine layer morphogenesis / STAT5 Activation / Co-inhibition by BTLA / COP9 signalosome / neurotrophin TRKA receptor binding / Activated NTRK2 signals through PI3K / transmembrane receptor protein tyrosine kinase adaptor activity / MET receptor recycling / 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 / positive regulation of actin filament polymerization / 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 / endodermal cell differentiation / GRB2:SOS provides linkage to MAPK signaling for Integrins / regulation of MAPK cascade / RHOU GTPase cycle / RET signaling / PI3K events in ERBB2 signaling / insulin receptor substrate binding / Interleukin-3, Interleukin-5 and GM-CSF signaling / PI3K Cascade / SOS-mediated signalling / Activated NTRK3 signals through RAS / Activated NTRK2 signals through RAS / signal transduction in response to DNA damage / SHC1 events in ERBB4 signaling / fibroblast growth factor receptor signaling pathway / Role of LAT2/NTAL/LAB on calcium mobilization / RHO GTPases Activate WASPs and WAVEs / Signalling to RAS / Interleukin receptor SHC signaling / GAB1 signalosome / Signal attenuation / Activated NTRK2 signals through FRS2 and FRS3 / SHC-related events triggered by IGF1R / SHC-mediated cascade:FGFR3 / MET activates RAS signaling / Schwann cell development / SHC-mediated cascade:FGFR2 / Signaling by PDGFRA transmembrane, juxtamembrane and kinase domain mutants / Signaling by PDGFRA extracellular domain mutants / SHC-mediated cascade:FGFR4 / Signaling by CSF3 (G-CSF) / Signaling by FGFR4 in disease / Erythropoietin activates RAS / SHC-mediated cascade:FGFR1 / FRS-mediated FGFR3 signaling / Signaling by FLT3 ITD and TKD mutants / FRS-mediated FGFR2 signaling / FRS-mediated FGFR4 signaling / Signaling by FGFR3 in disease / Tie2 Signaling / FRS-mediated FGFR1 signaling / Signaling by FGFR2 in disease / ephrin receptor binding / GRB2 events in EGFR signaling / SHC1 events in EGFR signaling / Signaling by FLT3 fusion proteins / FLT3 Signaling / phosphotyrosine residue binding / Signaling by FGFR1 in disease / myelination / EGFR Transactivation by Gastrin / NCAM signaling for neurite out-growth / FCERI mediated Ca+2 mobilization / GRB2 events in ERBB2 signaling / Downstream signal transduction / SHC1 events in ERBB2 signaling / Insulin receptor signalling cascade / insulin-like growth factor receptor signaling pathway / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / 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 / FCERI mediated MAPK activation / Regulation of signaling by CBL / Negative regulation of FGFR3 signaling / Negative regulation of FGFR2 signaling / Negative regulation of FGFR4 signaling
Similarity search - Function
GRB2, N-terminal SH3 domain / GRB2, C-terminal SH3 domain / Grb2-like / SH3 Domains / SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / SH2 domain superfamily ...GRB2, N-terminal SH3 domain / GRB2, C-terminal SH3 domain / Grb2-like / SH3 Domains / SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / SH2 domain superfamily / Src homology 3 domains / SH3 type barrels. / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Roll / Mainly Beta
Similarity search - Domain/homology
Growth factor receptor-bound protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsBolgov, A.A. / Korban, S.A. / Luzik, D.A. / Rogacheva, O.N. / Zhemkov, V.A. / Kim, M. / Skrynnikov, N.R. / Bezprozvanny, I.B.
Funding support Russian Federation, 1items
OrganizationGrant numberCountry
Russian Science Foundation19-15-00184 Russian Federation
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2020
Title: Crystal structure of the SH3 domain of growth factor receptor-bound protein 2.
Authors: Bolgov, A. / Korban, S. / Luzik, D. / Zhemkov, V. / Kim, M. / Rogacheva, O. / Bezprozvanny, I.
History
DepositionJul 26, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 29, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 8, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 24, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_radiation_wavelength.wavelength

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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: Growth factor receptor-bound protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,70311
Polymers13,8872
Non-polymers8159
Water1,44180
1
A: Growth factor receptor-bound protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,6058
Polymers6,9441
Non-polymers6627
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Growth factor receptor-bound protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,0973
Polymers6,9441
Non-polymers1542
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)97.731, 97.731, 51.032
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11B-227-

HOH

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Components

#1: Protein Growth factor receptor-bound protein 2 / Adapter protein GRB2 / Protein Ash / SH2/SH3 adapter GRB2


Mass: 6943.713 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Electron density is lacking for B58-B61 residues (C-terminal disordered region)
Source: (gene. exp.) Homo sapiens (human) / Gene: GRB2, ASH / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: P62993
#2: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 80 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.46 Å3/Da / Density % sol: 64.48 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1 M Hepes, 55% (v/v) MPD

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: Cryostream 800 (Oxford Cryosystems) / Serial crystal experiment: N
Diffraction sourceSource: SEALED TUBE / Type: OXFORD DIFFRACTION SUPERNOVA
Details: XtaLAB SuperNova (Rigaku Oxford Diffraction) with microfocused sealed tube
Wavelength: 1.54184 Å
DetectorType: RIGAKU HyPix-3000 / Detector: PIXEL / Date: May 27, 2019
Details: RIGAKU HyPix-3000 - High-resolution/high-speed 2D photon counting X-ray detector
RadiationMonochromator: Mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54184 Å / Relative weight: 1
ReflectionResolution: 2.5→48.865 Å / Num. obs: 6312 / % possible obs: 99.92 % / Redundancy: 1.892 % / Biso Wilson estimate: 17.82 Å2 / Rmerge(I) obs: 0.069 / Rpim(I) all: 0.045 / Rrim(I) all: 0.083 / Χ2: 1.05 / Net I/σ(I): 8.86
Reflection shellResolution: 2.5→2.5879 Å / Redundancy: 1.919 % / Rmerge(I) obs: 0.03 / Num. unique obs: 607

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Processing

Software
NameVersionClassification
PHENIX1.7.3_928refinement
CrysalisProdata reduction
CrysalisProdata scaling
MOLREPphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1GRI

1gri


Resolution: 2.5→28.212 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.99 / Phase error: 21.3
RfactorNum. reflection% reflectionSelection details
Rfree0.2101 292 -RANDOM
Rwork0.1597 ---
obs0.1621 6309 99.95 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Bsol: 27.199 Å2 / ksol: 0.356 e/Å3
Displacement parametersBiso max: 92.8 Å2 / Biso mean: 20.2 Å2 / Biso min: 0.24 Å2
Baniso -1Baniso -2Baniso -3
1-0.3042 Å2-0 Å2-0 Å2
2--0.3042 Å20 Å2
3----0.6084 Å2
Refinement stepCycle: final / Resolution: 2.5→28.212 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms957 0 47 80 1084
Biso mean--21.67 22.97 -
Num. residues----119
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011019
X-RAY DIFFRACTIONf_angle_d1.3911370
X-RAY DIFFRACTIONf_chiral_restr0.083136
X-RAY DIFFRACTIONf_plane_restr0.005173
X-RAY DIFFRACTIONf_dihedral_angle_d19.442384
LS refinement shellResolution: 2.5→2.5893 Å
RfactorNum. reflection% reflection
Rfree0.3079 36 -
Rwork0.2074 607 -
obs--100 %

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