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- PDB-1x1f: Solution structure of the PH domain of human Docking protein BRDG1 -

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Basic information

Entry
Database: PDB / ID: 1x1f
TitleSolution structure of the PH domain of human Docking protein BRDG1
ComponentsSignal-transducing adaptor protein 1
KeywordsSIGNALING PROTEIN / Docking protein BRDG1 / PH domain / structural genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


negative regulation of microglial cell migration / macrophage colony-stimulating factor receptor binding / negative regulation of macrophage colony-stimulating factor signaling pathway / negative regulation of ruffle assembly / positive regulation of B cell receptor signaling pathway / positive regulation of microglial cell mediated cytotoxicity / positive regulation of microglial cell activation / protein tyrosine kinase activator activity / positive regulation of phagocytosis, engulfment / negative regulation of macrophage chemotaxis ...negative regulation of microglial cell migration / macrophage colony-stimulating factor receptor binding / negative regulation of macrophage colony-stimulating factor signaling pathway / negative regulation of ruffle assembly / positive regulation of B cell receptor signaling pathway / positive regulation of microglial cell mediated cytotoxicity / positive regulation of microglial cell activation / protein tyrosine kinase activator activity / positive regulation of phagocytosis, engulfment / negative regulation of macrophage chemotaxis / negative regulation of phosphorylation / transmembrane receptor protein tyrosine kinase adaptor activity / centriolar satellite / signaling adaptor activity / cell surface receptor protein tyrosine kinase signaling pathway / phosphotyrosine residue binding / phospholipid binding / cellular response to lipopolysaccharide / positive regulation of gene expression / protein kinase binding / protein-containing complex / mitochondrion / nucleoplasm / nucleus / cytoplasm / cytosol
Similarity search - Function
STAP1, SH2 domain / Signal-transducing adaptor protein STAP1/STAP2 / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / PH domain / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / SH2 domain / Src homology 2 (SH2) domain profile. ...STAP1, SH2 domain / Signal-transducing adaptor protein STAP1/STAP2 / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / PH domain / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / 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
Signal-transducing adaptor protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsLi, H. / Tomizawa, T. / Koshiba, S. / Inoue, M. / Kigawa, T. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Solution structure of the PH domain of human Docking protein BRDG1
Authors: Li, H. / Tomizawa, T. / Koshiba, S. / Inoue, M. / Kigawa, T. / Yokoyama, S.
History
DepositionApr 4, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 4, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / 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_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.4May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Remark 650HELIX DETERMINATION METHOD: AUTHOR DETERMINED
Remark 700SHEET DETERMINATION METHOD: AUTHOR DETERMINED

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Signal-transducing adaptor protein 1


Theoretical massNumber of molelcules
Total (without water)17,0731
Polymers17,0731
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 / 100target function,structures with the least restraint violations
RepresentativeModel #1lowest energy

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Components

#1: Protein Signal-transducing adaptor protein 1 / STAP-1 / Stem cell adaptor protein 1 / BCR downstream signaling protein 1 / Docking protein BRDG1


Mass: 17073.367 Da / Num. of mol.: 1 / Fragment: PH domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: Cell-free protein synthesis / Gene: brdg1 / Plasmid: P040301-57 / References: UniProt: Q9ULZ2

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Experimental details

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Experiment

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

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Sample preparation

DetailsContents: 1.00mM PH domain U-13C, 15N; 20mM d-Tris-HCl(pH7.0); 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 90% H2O, 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 120mM / pH: 7 / Pressure: ambient / Temperature: 296 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.6Brukercollection
NMRPipe20031121Delaglio, F.processing
NMRView5.0.4Johnson, B. A.data analysis
KUJIRA0.913Kobayashi, N.data analysis
CYANA1.0.7Guentert, P.structure solution
CYANA1.0.7Guentert, P.refinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function,structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 20

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