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- PDB-2dcr: Fully automated solution structure determination of the Fes SH2 domain -

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Entry
Database: PDB / ID: 2dcr
TitleFully automated solution structure determination of the Fes SH2 domain
ComponentsProto-oncogene tyrosine-protein kinase Fes/Fps
KeywordsTRANSFERASE / SH2 domain / Fes / feline sarcoma oncogene / fully automated structure determination / FLYA algorithm
Function / homology
Function and homology information


positive regulation of myeloid cell differentiation / regulation of mast cell degranulation / regulation of vesicle-mediated transport / cellular response to vitamin D / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / CRMPs in Sema3A signaling / microtubule bundle formation / positive regulation of monocyte differentiation / regulation of cell motility / centrosome cycle ...positive regulation of myeloid cell differentiation / regulation of mast cell degranulation / regulation of vesicle-mediated transport / cellular response to vitamin D / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / CRMPs in Sema3A signaling / microtubule bundle formation / positive regulation of monocyte differentiation / regulation of cell motility / centrosome cycle / myoblast proliferation / cardiac muscle cell proliferation / regulation of cell differentiation / immunoglobulin receptor binding / Sema3A PAK dependent Axon repulsion / regulation of cell adhesion / positive regulation of microtubule polymerization / phosphatidylinositol binding / non-specific protein-tyrosine kinase / non-membrane spanning protein tyrosine kinase activity / Signaling by SCF-KIT / positive regulation of neuron projection development / peptidyl-tyrosine phosphorylation / cytoplasmic side of plasma membrane / chemotaxis / microtubule cytoskeleton / regulation of cell shape / regulation of cell population proliferation / cytoplasmic vesicle / protein tyrosine kinase activity / microtubule binding / protein autophosphorylation / cell adhesion / focal adhesion / Golgi apparatus / ATP binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Tyrosine-protein kinase, Fes/Fps type / Fes/Fps/Fer, SH2 domain / Fes/CIP4, and EFC/F-BAR homology domain / Fes/CIP4 homology domain / FCH domain / F-BAR domain / F-BAR domain profile. / AH/BAR domain superfamily / SH2 domain / SHC Adaptor Protein ...Tyrosine-protein kinase, Fes/Fps type / Fes/Fps/Fer, SH2 domain / Fes/CIP4, and EFC/F-BAR homology domain / Fes/CIP4 homology domain / FCH domain / F-BAR domain / F-BAR domain profile. / AH/BAR domain superfamily / SH2 domain / SHC Adaptor Protein / : / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / SH2 domain superfamily / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / Tyrosine-protein kinase, active site / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Tyrosine-protein kinase Fes/Fps
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / Fully automated NMR spectrum analysis, structure calculation without human intervention. Chemical shift assignments, conformational restraints have not been verified manually.
AuthorsLopez-Mendez, B. / Guntert, P.
Citation
Journal: J.AM.CHEM.SOC. / Year: 2006
Title: Automated protein structure determination from NMR spectra
Authors: Lopez-Mendez, B. / Guntert, P.
#1: Journal: J.Biomol.Nmr / Year: 2005
Title: Solution structure of the Src homology 2 domain from the human feline sarcoma oncogene Fes
Authors: Scott, A. / Pantoja-Uceda, D. / Koshiba, S. / Inoue, M. / Kigawa, T. / Terada, T. / Shirouzu, M. / Tanaka, A. / Sugano, S. / Yokoyama, S. / Guntert, P.
#2: Journal: J.Biomol.Nmr / Year: 2004
Title: NMR assignment of the SH2 domain from the human feline sarcoma oncogene FES
Authors: Scott, A. / Pantoja-Uceda, D. / Koshiba, S. / Inoue, M. / Kigawa, T. / Terada, T. / Shirouzu, M. / Tanaka, A. / Sugano, S. / Yokoyama, S.
History
DepositionJan 12, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 17, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_spectrometer ...database_2 / pdbx_nmr_spectrometer / 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_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.4May 29, 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: Proto-oncogene tyrosine-protein kinase Fes/Fps


Theoretical massNumber of molelcules
Total (without water)12,5061
Polymers12,5061
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)20 / 100structures with the least restraint violations
RepresentativeModel #1closest to the average

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Components

#1: Protein Proto-oncogene tyrosine-protein kinase Fes/Fps / C-Fes


Mass: 12506.106 Da / Num. of mol.: 1 / Fragment: SH2 DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: CELL-FREE PROTEIN SYNTHESIS / Plasmid: P040524-01 / Production host: Cell free synthesis / References: UniProt: P07332, EC: 2.7.1.112

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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

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Sample preparation

DetailsContents: 1.2MM UNIFORMLY 13C AND 15N LABELED PROTEIN; 20MM TRIS-HCL BUFFER; 100MM NACL; 1MM DITHIOTHREITOL; 0.02% NAN3
Sample conditionspH: 7 / Pressure: AMBIENT / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX6001
Bruker AVANCEBrukerAVANCE8002

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Processing

NMR software
NameVersionDeveloperClassification
FLYA1Lopez-Mendez, B,, Guntert, P.structure solution
CYANA2.1Guntert, P. et al.structure solution
OPALp1.2Koradi, R., Billeter, M., Guntert, P.refinement
RefinementMethod: Fully automated NMR spectrum analysis, structure calculation without human intervention. Chemical shift assignments, conformational restraints have not been verified manually.
Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 20

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