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- PDB-2d0n: Crystal structure of the C-terminal SH3 domain of the adaptor pro... -

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Basic information

Entry
Database: PDB / ID: 2d0n
TitleCrystal structure of the C-terminal SH3 domain of the adaptor protein GADS in complex with SLP-76 motif peptide reveals a unique SH3-SH3 interaction
Components
  • GRB2-related adaptor protein 2
  • SLP-76 binding peptide
KeywordsSIGNALING PROTEIN / SH3 DOMAIN-COMPLEX / MONA/GADS SH3C DOMAIN
Function / homology
Function and homology information


FLT3 Signaling / CD28 co-stimulation / FCERI mediated MAPK activation / Signaling by SCF-KIT / Generation of second messenger molecules / FCERI mediated Ca+2 mobilization / DAP12 signaling / regulation of MAPK cascade / phosphotyrosine residue binding / endosome ...FLT3 Signaling / CD28 co-stimulation / FCERI mediated MAPK activation / Signaling by SCF-KIT / Generation of second messenger molecules / FCERI mediated Ca+2 mobilization / DAP12 signaling / regulation of MAPK cascade / phosphotyrosine residue binding / endosome / signal transduction / nucleoplasm / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
GRAP2, C-terminal SH3 domain / 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 ...GRAP2, C-terminal SH3 domain / 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
GRB2-related adaptor protein 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.57 Å
AuthorsDimasi, N.
CitationJournal: Int.J.Biochem.Cell Biol. / Year: 2007
Title: Crystal structure of the C-terminal SH3 domain of the adaptor protein GADS in complex with SLP-76 motif peptide reveals a unique SH3-SH3 interaction
Authors: Dimasi, N.
History
DepositionAug 4, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 23, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GRB2-related adaptor protein 2
B: SLP-76 binding peptide
C: GRB2-related adaptor protein 2
D: SLP-76 binding peptide


Theoretical massNumber of molelcules
Total (without water)15,4434
Polymers15,4434
Non-polymers00
Water3,585199
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.622, 58.622, 74.098
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212
Components on special symmetry positions
IDModelComponents
11A-5-

HOH

21A-138-

HOH

31A-189-

HOH

41C-102-

HOH

51D-128-

HOH

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Components

#1: Protein GRB2-related adaptor protein 2 / GADS protein / Growth factor receptor binding protein / GRBLG / GRB-2-like protein / GRB2L / ...GADS protein / Growth factor receptor binding protein / GRBLG / GRB-2-like protein / GRB2L / Hematopoietic cell-associated adaptor protein GrpL / GRB-2-related monocytic adapter protein / Monocytic adapter / MONA / Adapter protein GRID


Mass: 6719.488 Da / Num. of mol.: 2 / Fragment: C-terminal SH3 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pT7-GADS-cSH3 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O89100
#2: Protein/peptide SLP-76 binding peptide


Mass: 1002.123 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: The SLP-76 peptide was synthesized synthetically with the F-moc chemistry
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 199 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.08 Å3/Da / Density % sol: 42.04 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 1.26M ammonium sulfate, 0.1M cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 0.9 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 13, 2005
RadiationMonochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.54→36.18 Å / Num. obs: 16893 / % possible obs: 85.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.043 / Rsym value: 0.178
Reflection shellResolution: 1.54→1.59 Å / Rmerge(I) obs: 0.043 / % possible all: 85.1

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Processing

Software
NameClassification
HKL-2000data collection
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1OEB Chain A

1oeb


Resolution: 1.57→7.9 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.284 826 RANDOM
Rwork0.221 --
obs0.221 16886 -
all-19749 -
Refinement stepCycle: LAST / Resolution: 1.57→7.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1059 0 0 199 1258
LS refinement shellHighest resolution: 1.57 Å

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