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- PDB-2azs: NMR structure of the N-terminal SH3 domain of Drk (calculated wit... -

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Basic information

Entry
Database: PDB / ID: 2azs
TitleNMR structure of the N-terminal SH3 domain of Drk (calculated without NOE restraints)
ComponentsSH2-SH3 adapter protein drk
KeywordsSIGNALING PROTEIN / Drosophila melanogaster / SH3 fragment / DRK
Function / homology
Function and homology information


sevenless binding / PI3K Cascade / Generation of second messenger molecules / PI-3K cascade:FGFR1 / PI-3K cascade:FGFR2 / PI-3K cascade:FGFR3 / PI-3K cascade:FGFR4 / Erythropoietin activates RAS / Signaling by CSF3 (G-CSF) / SOS-mediated signalling ...sevenless binding / PI3K Cascade / Generation of second messenger molecules / PI-3K cascade:FGFR1 / PI-3K cascade:FGFR2 / PI-3K cascade:FGFR3 / PI-3K cascade:FGFR4 / Erythropoietin activates RAS / Signaling by CSF3 (G-CSF) / SOS-mediated signalling / Signaling by SCF-KIT / Regulation of KIT signaling / Signalling to RAS / Downstream signal transduction / DAP12 signaling / SHC-related events triggered by IGF1R / Role of LAT2/NTAL/LAB on calcium mobilization / FCERI mediated Ca+2 mobilization / SHC-mediated cascade:FGFR1 / FRS-mediated FGFR1 signaling / SHC-mediated cascade:FGFR2 / FRS-mediated FGFR2 signaling / SHC-mediated cascade:FGFR3 / FRS-mediated FGFR3 signaling / FRS-mediated FGFR4 signaling / SHC-mediated cascade:FGFR4 / Signal attenuation / Insulin receptor signalling cascade / RET signaling / FLT3 Signaling / FCERI mediated MAPK activation / PIP3 activates AKT signaling / GAB1 signalosome / PI3K events in ERBB2 signaling / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / SHC1 events in ERBB4 signaling / GRB2 events in EGFR signaling / SHC1 events in EGFR signaling / GRB2 events in ERBB2 signaling / EGFR Transactivation by Gastrin / torso signaling pathway / NCAM signaling for neurite out-growth / tracheal outgrowth, open tracheal system / R7 cell fate commitment / Spry regulation of FGF signaling / Negative regulation of FGFR1 signaling / Negative regulation of FGFR2 signaling / Negative regulation of FGFR3 signaling / Negative regulation of FGFR4 signaling / Regulation of signaling by CBL / sevenless signaling pathway / RAF/MAP kinase cascade / EGFR downregulation / RHOU GTPase cycle / Cargo recognition for clathrin-mediated endocytosis / RHO GTPases Activate WASPs and WAVEs / epithelial cell migration, open tracheal system / Regulation of actin dynamics for phagocytic cup formation / follicle cell of egg chamber development / Clathrin-mediated endocytosis / imaginal disc-derived wing morphogenesis / short-term memory / olfactory learning / COP9 signalosome / epidermal growth factor receptor binding / regulation of MAPK cascade / associative learning / positive regulation of cell size / fibroblast growth factor receptor signaling pathway / vascular endothelial growth factor receptor signaling pathway / phosphotyrosine residue binding / positive regulation of TORC1 signaling / sensory perception of sound / epidermal growth factor receptor signaling pathway / positive regulation of receptor-mediated endocytosis / signaling receptor complex adaptor activity / insulin receptor signaling pathway / presynapse / Ras protein signal transduction / positive regulation of ERK1 and ERK2 cascade / signal transduction / protein-containing complex / nucleoplasm / plasma membrane / cytoplasm
Similarity search - Function
Grb2-like / SH3 Domains / 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 ...Grb2-like / SH3 Domains / 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 / Roll / Mainly Beta
Similarity search - Domain/homology
Growth factor receptor-bound protein 2
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodSOLUTION NMR / simulated annealing
AuthorsBezsonova, I. / Singer, A.U. / Choy, W.-Y. / Tollinger, M. / Forman-Kay, J.D.
CitationJournal: Biochemistry / Year: 2005
Title: Structural Comparison of the Unstable drkN SH3 Domain and a Stable Mutant
Authors: Bezsonova, I. / Singer, A. / Choy, W.-Y. / Tollinger, M. / Forman-Kay, J.D.
History
DepositionSep 12, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 13, 2005Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SH2-SH3 adapter protein drk


Theoretical massNumber of molelcules
Total (without water)6,8691
Polymers6,8691
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein SH2-SH3 adapter protein drk / Protein enhancer of sevenless 2B / Downstream of receptor kinase / Protein Esev 2B


Mass: 6868.628 Da / Num. of mol.: 1 / Fragment: N-Terminal SH3 domain, residues 1-59
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: drk, E sev 2B / Plasmid: PET-11A / Production host: Escherichia coli (E. coli) / Strain (production host): HMS174 / References: UniProt: Q08012

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111H/D amide exchange
121HNCO-based 3D experiments (non-TROSY)
1312D Ca-Cb RDC experiment
141Ca-Ha RDC experiment
151HNCO experiment
161HN-Ha J-coupling experiment
1713D HN(CO)HB

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Sample preparation

DetailsContents: 1mM DRKN SH3 domain 15N, 13C, 500 mM NA2SO4, 50mM Phosphate, 90% H2O, 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 500 mM / pH: 6 / Pressure: 1 atm / Temperature: 293 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 500 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CNS1Brunger, A.T. et al.refinement
CNS1Brunger, A.T. et al.structure determination
RefinementMethod: simulated annealing / Software ordinal: 1
Details: THE STRUCTURES ARE BASED ON RESIDUAL DIPOLAR COUPLING RESTRAINTS,CARBONYL CHEMICAL SHIFT ANISOTROPY RESTRAINTS, DIHEDRAL ANGLE RESTRAINTS AND HYDROGEN BOND RESTRAINTS
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 10

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