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- PDB-6vk2: NMR solution structure of Grb2-SH2 domain at pH 7 -

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Basic information

Entry
Database: PDB / ID: 6vk2
TitleNMR solution structure of Grb2-SH2 domain at pH 7
ComponentsGrowth factor receptor-bound protein 2GRB2
KeywordsCELL CYCLE / Grb2 / SH2 domain / dynamics
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 / vesicle membrane / neurotrophin TRKA receptor binding / Activated NTRK2 signals through PI3K / MET receptor recycling / transmembrane receptor protein tyrosine kinase adaptor activity ...guanyl-nucleotide exchange factor adaptor activity / Grb2-EGFR complex / branching involved in labyrinthine layer morphogenesis / STAT5 Activation / COP9 signalosome / vesicle membrane / 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 / 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 / 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 / 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 / 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 / Negative regulation of FGFR4 signaling / EGFR downregulation / Negative regulation of FGFR1 signaling / Signaling by ERBB2 TMD/JMD mutants / B cell receptor signaling pathway
Similarity search - Function
GRB2, N-terminal SH3 domain / GRB2, C-terminal SH3 domain / Grb2-like / SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / Src homology 3 domains / SH2 domain superfamily ...GRB2, N-terminal SH3 domain / GRB2, C-terminal SH3 domain / Grb2-like / 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
Similarity search - Domain/homology
Growth factor receptor-bound protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / na
AuthorsSanches, K. / Caruso, I.P. / Melo, F.A. / Almeida, F.C.L.
Funding support Brazil, 4items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)2014/17630-0 Brazil
Sao Paulo Research Foundation (FAPESP)2017/20642-8 Brazil
Brazilian National Council for Scientific and Technological Development (CNPq)442951/2014-0 Brazil
Brazilian National Council for Scientific and Technological Development (CNPq)309564/2017-4 Brazil
Citation
Journal: Sci Rep / Year: 2020
Title: The dynamics of free and phosphopeptide-bound Grb2-SH2 reveals two dynamically independent subdomains and an encounter complex with fuzzy interactions.
Authors: Sanches, K. / Caruso, I.P. / Almeida, F.C.L. / Melo, F.A.
#1: Journal: Biomol NMR Assign / Year: 2019
Title: NMR assignment of free 1H, 15N and 13C-Grb2-SH2 domain.
Authors: Sanches, K. / Caruso, I.P. / Almeida, F.C.L. / Melo, F.A.
History
DepositionJan 18, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 29, 2020Provider: repository / Type: Initial release
Revision 1.1Aug 5, 2020Group: Database references / Category: database_2 / pdbx_database_related / Item: _database_2.database_code
Revision 1.2Aug 19, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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.year / _citation_author.identifier_ORCID
Revision 1.3Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Growth factor receptor-bound protein 2


Theoretical massNumber of molelcules
Total (without water)11,2051
Polymers11,2051
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 66317structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

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


Mass: 11204.756 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GRB2, ASH / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P62993

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
121isotropic13D 1H-13C NOESY aliphatic
131isotropic13D 1H-13C NOESY aromatic
141isotropic13D 1H-15N NOESY
151isotropic23D HN(CA)CB
161isotropic33D HNCA
171isotropic23D CBCA(CO)NH
181isotropic23D HBHA(CO)NH
191isotropic23D HNCO
1101isotropic23D H(CCO)NH
1111isotropic23D (H)CCH-TOCSY

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Sample preparation

DetailsType: solution
Contents: 200 mM sodium chloride, 20 mM sodium phosphate, 1 mM EDTA, 1 mM PMSF, 5 mM sodium azide, 300 uM [U-100% 13C; U-100% 15N] Grb2-SH2, 90% H2O/10% D2O
Details: ~300 uM 13C/15N-Grb2-SH2 in buffer 20 mM NaPi pH 7.0 containing 200 mM NaCl, 1.0 mM EDTA, 1.0 mM PMSF, 5.0 mM NaN3, and 10% D2O
Label: Grb2-SH2 / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
200 mMsodium chloridenatural abundance1
20 mMsodium phosphatenatural abundance1
1 mMEDTAnatural abundance1
1 mMPMSFnatural abundance1
5 mMsodium azidenatural abundance1
300 uMGrb2-SH2[U-100% 13C; U-100% 15N]1
Sample conditionsDetails: ~300 uM 13C/15N-Grb2-SH2 in buffer 20 mM NaPi pH 7.0 containing 200 mM NaCl, 1.0 mM EDTA, 1.0 mM PMSF, 5.0 mM NaN3, and 10% D2O
Ionic strength: 138.2 mM / Label: Condition1 / pH: 7 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE III HDBrukerAVANCE III HD9001
Bruker AVANCE IIIBrukerAVANCE III8002
Bruker AVANCE III HDBrukerAVANCE III HD7003

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Processing

NMR software
NameVersionDeveloperClassification
CS-ROSETTA3.3Shen, Vernon, Baker and Baxstructure calculation
CcpNmr AnalysisCCPNdata analysis
ARIALinge, O'Donoghue and Nilgesstructure calculation
CS-ROSETTAShen, Vernon, Baker and Baxrefinement
CcpNmr AnalysisCCPNchemical shift assignment
CcpNmr AnalysisCCPNpeak picking
RefinementMethod: na / Software ordinal: 4
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 66317 / Conformers submitted total number: 20

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