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- PDB-1n3h: Coupling of Folding and Binding in the PTB Domain of the Signalin... -

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Basic information

Entry
Database: PDB / ID: 1n3h
TitleCoupling of Folding and Binding in the PTB Domain of the Signaling Protein Shc
ComponentsSHC Transforming protein
KeywordsSIGNALING PROTEIN / Free Protein / Beta Sandwich
Function / homology
Function and homology information


regulation of superoxide metabolic process / positive regulation of cell proliferation in bone marrow / XBP1(S) activates chaperone genes / neurotrophin TRKA receptor binding / transmembrane receptor protein tyrosine kinase adaptor activity / Interleukin-15 signaling / Shc-EGFR complex / Interleukin-2 signaling / epidermal growth factor binding / epidermal growth factor receptor binding ...regulation of superoxide metabolic process / positive regulation of cell proliferation in bone marrow / XBP1(S) activates chaperone genes / neurotrophin TRKA receptor binding / transmembrane receptor protein tyrosine kinase adaptor activity / Interleukin-15 signaling / Shc-EGFR complex / Interleukin-2 signaling / epidermal growth factor binding / epidermal growth factor receptor binding / Signaling by ALK / Signaling by ALK fusions and activated point mutants / Activated NTRK3 signals through RAS / RET signaling / Activated NTRK2 signals through RAS / Interleukin-3, Interleukin-5 and GM-CSF signaling / SHC1 events in ERBB4 signaling / Signalling to RAS / SHC-related events triggered by IGF1R / Role of LAT2/NTAL/LAB on calcium mobilization / Signal attenuation / Interleukin receptor SHC signaling / SHC-mediated cascade:FGFR3 / MET activates RAS signaling / SHC-mediated cascade:FGFR2 / SHC-mediated cascade:FGFR4 / SHC-mediated cascade:FGFR1 / Erythropoietin activates RAS / Signaling by CSF3 (G-CSF) / Tie2 Signaling / insulin-like growth factor receptor binding / SHC1 events in EGFR signaling / phosphotyrosine residue binding / ephrin receptor binding / SHC1 events in ERBB2 signaling / Integrin signaling / Insulin receptor signalling cascade / Constitutive Signaling by Overexpressed ERBB2 / negative regulation of angiogenesis / FCERI mediated Ca+2 mobilization / insulin-like growth factor receptor signaling pathway / phospholipid binding / FCERI mediated MAPK activation / Signaling by ERBB2 TMD/JMD mutants / Constitutive Signaling by EGFRvIII / insulin receptor binding / Signaling by ERBB2 ECD mutants / epidermal growth factor receptor signaling pathway / Signaling by ERBB2 KD Mutants / cell-cell adhesion / receptor tyrosine kinase binding / cellular response to growth factor stimulus / GPER1 signaling / Signaling by CSF1 (M-CSF) in myeloid cells / Constitutive Signaling by Ligand-Responsive EGFR Cancer Variants / DAP12 signaling / insulin receptor signaling pathway / heart development / actin cytoskeleton organization / RAF/MAP kinase cascade / angiogenesis / Extra-nuclear estrogen signaling / positive regulation of MAPK cascade / positive regulation of ERK1 and ERK2 cascade / mitochondrial matrix / intracellular signal transduction / defense response to bacterium / focal adhesion / negative regulation of DNA-templated transcription / positive regulation of cell population proliferation / negative regulation of apoptotic process / positive regulation of DNA-templated transcription / plasma membrane / cytosol
Similarity search - Function
Phosphotyrosine interaction domain, Shc-like / SH2 adaptor protein C, SH2 domain / Phosphotyrosine interaction domain (PTB/PID) / Phosphotyrosine interaction domain (PID) profile. / Phosphotyrosine-binding domain, phosphotyrosine-interaction (PI) domain / PTB/PI domain / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / SH2 domain / Src homology 2 (SH2) domain profile. ...Phosphotyrosine interaction domain, Shc-like / SH2 adaptor protein C, SH2 domain / Phosphotyrosine interaction domain (PTB/PID) / Phosphotyrosine interaction domain (PID) profile. / Phosphotyrosine-binding domain, phosphotyrosine-interaction (PI) domain / PTB/PI domain / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / SH2 domain superfamily / PH-like domain superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
SHC-transforming protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / Distance Geometry, Simulated Annealing, Molecular Dynamics, ARIA
AuthorsFarooq, A. / Zeng, L. / Yan, K.S. / Ravichandran, K.S. / Zhou, M.-M.
CitationJournal: Structure / Year: 2003
Title: Coupling of Folding and Binding in the PTB Domain of the Signaling Protein Shc
Authors: Farooq, A. / Zeng, L. / Yan, K.S. / Ravichandran, K.S. / Zhou, M.-M.
History
DepositionOct 28, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 28, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SHC Transforming protein


Theoretical massNumber of molelcules
Total (without water)22,6571
Polymers22,6571
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / 200
Representative

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Components

#1: Protein SHC Transforming protein


Mass: 22657.021 Da / Num. of mol.: 1 / Fragment: PTB domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: Shc / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P29353

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-separated NOESY
1213D 15N-separated NOESY
131HNHA

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Sample preparation

DetailsContents: 0.5mM Shc PTB Domain, 50mM Sodium phosphate, 20mM DTT-d10, pH 6.5
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 200mM / pH: 6.5 / Pressure: 1 atm / Temperature: 308 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipe3.1Delaglioprocessing
X-PLOR3.1Brungerstructure solution
XwinNMR3.1collection
ARIA1.1Niiges, M.structure solution
X-PLOR3.1Brungerrefinement
RefinementMethod: Distance Geometry, Simulated Annealing, Molecular Dynamics, ARIA
Software ordinal: 1
NMR ensembleConformers calculated total number: 200 / Conformers submitted total number: 1

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