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- PDB-1kfz: Solution Structure of C-terminal Sem-5 SH3 Domain (Ensemble of 16... -

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Entry
Database: PDB / ID: 1kfz
TitleSolution Structure of C-terminal Sem-5 SH3 Domain (Ensemble of 16 Structures)
ComponentsSEX MUSCLE ABNORMAL PROTEIN 5
KeywordsSIGNALING PROTEIN / All beta protein
Function / homology
Function and homology information


Signaling by SCF-KIT / Regulation of KIT signaling / GRB2 events in ERBB2 signaling / GRB2:SOS provides linkage to MAPK signaling for Integrins / NCAM signaling for neurite out-growth / SHC-mediated cascade:FGFR1 / PI-3K cascade:FGFR1 / FRS-mediated FGFR1 signaling / SHC-mediated cascade:FGFR2 / FRS-mediated FGFR2 signaling ...Signaling by SCF-KIT / Regulation of KIT signaling / GRB2 events in ERBB2 signaling / GRB2:SOS provides linkage to MAPK signaling for Integrins / NCAM signaling for neurite out-growth / SHC-mediated cascade:FGFR1 / PI-3K 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 / PI-3K cascade:FGFR4 / Insulin receptor signalling cascade / MET activates RAS signaling / MET activates PI3K/AKT signaling / RHOU GTPase cycle / FLT3 Signaling / PIP3 activates AKT signaling / GRB2 events in EGFR signaling / SHC1 events in EGFR signaling / PI3K events in ERBB2 signaling / Regulation of actin dynamics for phagocytic cup formation / EGFR Transactivation by Gastrin / RHO GTPases Activate WASPs and WAVEs / RAF/MAP kinase cascade / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / regulation of cell projection organization / Downstream signal transduction / MET activates RAP1 and RAC1 / MET receptor recycling / regulation of nematode larval development / Negative regulation of MET activity / EGFR downregulation / Cargo recognition for clathrin-mediated endocytosis / Regulation of signaling by CBL / Clathrin-mediated endocytosis / regulation of vulval development / male genitalia development / COP9 signalosome / epidermal growth factor receptor binding / muscle organ development / regulation of MAPK cascade / regulation of cell migration / phosphotyrosine residue binding / epidermal growth factor receptor signaling pathway / signal transduction / 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 / SH3 type barrels. / SH2 domain / 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 / SH3 type barrels. / SH2 domain / 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
Sex muscle abnormal protein 5
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
MethodSOLUTION NMR / distance geometry, simulated annealing, molecular dynamics
AuthorsFerreon, J.C. / Volk, D.E. / Luxon, B.A. / Gorenstein, D. / Hilser, V.J.
CitationJournal: Biochemistry / Year: 2003
Title: Solution Structure, Dynamics and Thermodynamics of the Native State Ensemble of Sem-5 C-Terminal SH3 Domain
Authors: Ferreon, J.C. / Volk, D.E. / Luxon, B.A. / Gorenstein, D. / Hilser, V.J.
History
DepositionNov 24, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 20, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
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: SEX MUSCLE ABNORMAL PROTEIN 5


Theoretical massNumber of molelcules
Total (without water)7,2381
Polymers7,2381
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)16 / 50structures with the least restraint violations,structures with the lowest energy
RepresentativeModel #2lowest energy

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Components

#1: Protein SEX MUSCLE ABNORMAL PROTEIN 5


Mass: 7237.967 Da / Num. of mol.: 1 / Fragment: C-TERMINAL SH3 Domain (RESIDUES 155-214) / Mutation: C209A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: Sem-5 / Plasmid: pet19b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 pLysS / References: UniProt: P29355

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Experimental details

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Experiment

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

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Sample preparation

DetailsContents: 1mM Sem-5 SH3 domain, both 15N, and 15N,13C labeled, 50 mM sodium acetate buffer, 10 mM CaCl2, 100 mM NaCl, pH 4.8, 90%H2O, 10%D2O
Solvent system: 90%H20, 10%D2O
Sample conditionsIonic strength: 100 mM NaCl / pH: 4.8 / Pressure: ambient / Temperature: 298 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: Varian UNITYPLUS / Manufacturer: Varian / Model: UNITYPLUS / Field strength: 400 MHz

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Processing

NMR software
NameVersionDeveloperClassification
Felixv.98MSIprocessing
VNMR1Variancollection
CNS1Brunger, et al.structure solution
CNS1Brunger, et al.refinement
RefinementMethod: distance geometry, simulated annealing, molecular dynamics
Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations,structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 16

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