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- PDB-2h46: Native domain-swapped dimer crystal structure of the Grb2 SH2 domain -

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Basic information

Entry
Database: PDB / ID: 2h46
TitleNative domain-swapped dimer crystal structure of the Grb2 SH2 domain
ComponentsGrowth Receptor Binding Protein 2
KeywordsHORMONE/GROWTH FACTOR / helix-sheet-helix / HORMONE-GROWTH FACTOR COMPLEX
Function / homology
Function and homology information


guanyl-nucleotide exchange factor adaptor activity / Grb2-EGFR complex / branching involved in labyrinthine layer morphogenesis / STAT5 Activation / COP9 signalosome / neurotrophin TRKA receptor binding / Activated NTRK2 signals through PI3K / MET receptor recycling / transmembrane receptor protein tyrosine kinase adaptor activity / Signaling by cytosolic FGFR1 fusion mutants ...guanyl-nucleotide exchange factor adaptor activity / Grb2-EGFR complex / branching involved in labyrinthine layer morphogenesis / STAT5 Activation / COP9 signalosome / neurotrophin TRKA receptor binding / Activated NTRK2 signals through PI3K / 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 / vesicle membrane / Costimulation by the CD28 family / CD28 dependent Vav1 pathway / Signaling by LTK / MET activates PI3K/AKT signaling / Signal regulatory protein family interactions / natural killer cell mediated cytotoxicity / Regulation of KIT signaling / epidermal growth factor receptor binding / PI-3K cascade:FGFR3 / positive regulation of actin filament polymerization / PI-3K cascade:FGFR2 / STAT5 activation downstream of FLT3 ITD mutants / PI-3K cascade:FGFR4 / PI-3K cascade:FGFR1 / endodermal cell differentiation / GRB2:SOS provides linkage to MAPK signaling for Integrins / RHOU GTPase cycle / regulation of MAPK cascade / PI3K events in ERBB2 signaling / RET signaling / SOS-mediated signalling / Interleukin-3, Interleukin-5 and GM-CSF signaling / insulin receptor substrate binding / Activated NTRK3 signals through RAS / Activated NTRK2 signals through RAS / PI3K Cascade / SHC1 events in ERBB4 signaling / Signalling to RAS / signal transduction in response to DNA damage / RHO GTPases Activate WASPs and WAVEs / fibroblast growth factor receptor signaling pathway / GAB1 signalosome / Role of LAT2/NTAL/LAB on calcium mobilization / SHC-related events triggered by IGF1R / Activated NTRK2 signals through FRS2 and FRS3 / Interleukin receptor SHC signaling / Signal attenuation / SHC-mediated cascade:FGFR3 / MET activates RAS signaling / Signaling by PDGFRA transmembrane, juxtamembrane and kinase domain mutants / Signaling by PDGFRA extracellular domain mutants / SHC-mediated cascade:FGFR2 / Schwann cell development / SHC-mediated cascade:FGFR4 / Signaling by FGFR4 in disease / Erythropoietin activates RAS / SHC-mediated cascade:FGFR1 / 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 / Tie2 Signaling / FRS-mediated FGFR1 signaling / Signaling by FGFR2 in disease / GRB2 events in EGFR signaling / SHC1 events in EGFR signaling / EGFR Transactivation by Gastrin / Signaling by FLT3 fusion proteins / FLT3 Signaling / ephrin receptor binding / Signaling by FGFR1 in disease / myelination / GRB2 events in ERBB2 signaling / phosphotyrosine residue binding / NCAM signaling for neurite out-growth / SHC1 events in ERBB2 signaling / Downstream signal transduction / Constitutive Signaling by Overexpressed ERBB2 / Insulin receptor signalling cascade / FCERI mediated Ca+2 mobilization / insulin-like growth factor receptor signaling pathway / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / T cell activation / InlB-mediated entry of Listeria monocytogenes into host cell / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / cellular response to ionizing radiation / Regulation of signaling by CBL / FCERI mediated MAPK activation / Negative regulation of FGFR3 signaling / FCGR3A-mediated phagocytosis / B cell receptor signaling pathway / Signaling by ERBB2 TMD/JMD mutants / Negative regulation of FGFR2 signaling / EGFR downregulation
Similarity search - Function
GRB2, N-terminal SH3 domain / GRB2, C-terminal SH3 domain / Grb2-like / SH2 domain / SHC Adaptor Protein / SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain ...GRB2, N-terminal SH3 domain / GRB2, C-terminal SH3 domain / Grb2-like / SH2 domain / SHC Adaptor Protein / SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / Src homology 3 domains / SH2 domain superfamily / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Growth factor receptor-bound protein 2 / GRB2 protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsBenfield, A.P. / Martin, S.F. / Whiddon, B.B.
CitationJournal: Arch.Biochem.Biophys. / Year: 2007
Title: Structural and energetic aspects of Grb2-SH2 domain-swapping.
Authors: Benfield, A.P. / Whiddon, B.B. / Clements, J.H. / Martin, S.F.
History
DepositionMay 23, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 6, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _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

Downloads & links

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Assembly

Deposited unit
E: Growth Receptor Binding Protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,7802
Polymers13,6871
Non-polymers921
Water1,29772
1
E: Growth Receptor Binding Protein 2
hetero molecules

E: Growth Receptor Binding Protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,5594
Polymers27,3752
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_556-x,y,-z+11
Buried area5510 Å2
ΔGint-27 kcal/mol
Surface area11680 Å2
MethodPISA
2
E: Growth Receptor Binding Protein 2
hetero molecules
x 8


Theoretical massNumber of molelcules
Total (without water)110,23616
Polymers109,5008
Non-polymers7378
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_575-x,-y+2,z1
crystal symmetry operation3_665-y+1,x+1,z1
crystal symmetry operation4_465y-1,-x+1,z1
crystal symmetry operation5_556-x,y,-z+11
crystal symmetry operation6_576x,-y+2,-z+11
crystal symmetry operation7_466y-1,x+1,-z+11
crystal symmetry operation8_666-y+1,-x+1,-z+11
Buried area32590 Å2
ΔGint-163 kcal/mol
Surface area36170 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)80.783, 80.783, 75.216
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number97
Space group name H-MI422
Components on special symmetry positions
IDModelComponents
11E-228-

HOH

21E-235-

HOH

31E-239-

HOH

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Components

#1: Protein Growth Receptor Binding Protein 2 / Grb2


Mass: 13687.465 Da / Num. of mol.: 1 / Fragment: SH2 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GRB2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6ICN0, UniProt: P62993*PLUS
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 72 / Source method: isolated from a natural source / Formula: H2O

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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: 2.38 Å3/Da / Density % sol: 48.42 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 15 mg/mL Grb2-SH2 in 50 mM HEPES at pH 7.5 mixed with equal volume of 100 mM MES and 2.1 M NH4SO4 at pH 6.0. , pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jan 1, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→30 Å / Num. obs: 10060 / % possible obs: 99.5 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Rmerge(I) obs: 0.035 / Χ2: 1.255 / Net I/σ(I): 37.2
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.9-1.970.3049811.2531100
1.97-2.050.2179941.4921100
2.05-2.140.1559951.1321100
2.14-2.250.1189861.404199.9
2.25-2.390.0969881.391199.9
2.39-2.580.06810101.1321100
2.58-2.840.05210101.0141100
2.84-3.250.03710161.217199.8
3.25-4.090.02710201.382199.5
4.09-300.02110601.14196.2

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Phasing

Phasing MRRfactor: 0.485 / Cor.coef. Fo:Fc: 0.5
Highest resolutionLowest resolution
Rotation4 Å18.35 Å
Translation4 Å18.35 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
CNSrefinement
PDB_EXTRACT2data extraction
MAR345data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→30 Å / FOM work R set: 0.831 / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.231 521 5.1 %Random
Rwork0.222 ---
all0.22 ---
obs0.22 10052 99.4 %-
Solvent computationBsol: 60.619 Å2
Displacement parametersBiso mean: 34.989 Å2
Baniso -1Baniso -2Baniso -3
1-6.332 Å20 Å20 Å2
2--6.332 Å20 Å2
3----12.664 Å2
Refinement stepCycle: LAST / Resolution: 1.9→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms809 0 6 72 887
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_d1.268
X-RAY DIFFRACTIONc_mcbond_it1.6151.5
X-RAY DIFFRACTIONc_scbond_it2.0492
X-RAY DIFFRACTIONc_mcangle_it2.6762
X-RAY DIFFRACTIONc_scangle_it3.1392.5
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs
1.9-1.970.343440.289928972
1.97-2.050.26530.238937990
2.05-2.140.258530.236940993
2.14-2.250.282470.23941988
2.25-2.390.326400.24953993
2.39-2.580.324610.2339441005
2.58-2.840.31570.2379551012
2.84-3.250.203560.2259631019
3.25-4.090.194600.1899611021
4.09-400.188500.22410091059
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.paramCNS_TOPPAR:protein.top
X-RAY DIFFRACTION2CNS_TOPPAR:dna-rna_rep.paramCNS_TOPPAR:dna-rna.top
X-RAY DIFFRACTION3CNS_TOPPAR:water_rep.paramCNS_TOPPAR:water.top
X-RAY DIFFRACTION4CNS_TOPPAR:ion.paramCNS_TOPPAR:ion.top
X-RAY DIFFRACTION5gly.paramgly.top

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