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- PDB-1r1s: Structural Basis for Differential Recognition of Tyrosine Phospho... -

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Basic information

Entry
Database: PDB / ID: 1r1s
TitleStructural Basis for Differential Recognition of Tyrosine Phosphorylated Sites in the Linker for Activation of T cells (LAT) by the Adaptor Protein Gads
Components
  • GRB2-related adaptor protein 2
  • LAT pY226 peptide
KeywordsPEPTIDE BINDING PROTEIN / SH2 / Gads / LAT / phosphopeptide
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 / SH2 domain / SHC Adaptor Protein / SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / Src homology 3 domains ...GRAP2, C-terminal SH3 domain / Grb2-like / SH2 domain / SHC Adaptor Protein / SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / Src homology 3 domains / SH2 domain superfamily / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
GRB2-related adaptor protein 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsCho, S. / Mariuzza, R.A.
CitationJournal: Embo J. / Year: 2004
Title: Structural basis for differential recognition of tyrosine-phosphorylated sites in the linker for activation of T cells (LAT) by the adaptor Gads.
Authors: Cho, S. / Velikovsky, C.A. / Swaminathan, C.P. / Houtman, J.C. / Samelson, L.E. / Mariuzza, R.A.
History
DepositionSep 24, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 28, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GRB2-related adaptor protein 2
B: LAT pY226 peptide
C: GRB2-related adaptor protein 2
D: LAT pY226 peptide
E: GRB2-related adaptor protein 2
F: LAT pY226 peptide
G: GRB2-related adaptor protein 2
H: LAT pY226 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,38915
Polymers50,7168
Non-polymers6727
Water7,945441
1
A: GRB2-related adaptor protein 2
B: LAT pY226 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,8714
Polymers12,6792
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1550 Å2
ΔGint-44 kcal/mol
Surface area6240 Å2
MethodPISA
2
C: GRB2-related adaptor protein 2
D: LAT pY226 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,8714
Polymers12,6792
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1460 Å2
ΔGint-36 kcal/mol
Surface area6150 Å2
MethodPISA
3
E: GRB2-related adaptor protein 2
F: LAT pY226 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,8714
Polymers12,6792
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1260 Å2
ΔGint-24 kcal/mol
Surface area6410 Å2
MethodPISA
4
G: GRB2-related adaptor protein 2
H: LAT pY226 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,7753
Polymers12,6792
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1150 Å2
ΔGint-18 kcal/mol
Surface area6290 Å2
MethodPISA
5
A: GRB2-related adaptor protein 2
B: LAT pY226 peptide
E: GRB2-related adaptor protein 2
F: LAT pY226 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,7428
Polymers25,3584
Non-polymers3844
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4930 Å2
ΔGint-89 kcal/mol
Surface area10540 Å2
MethodPISA
6
C: GRB2-related adaptor protein 2
D: LAT pY226 peptide
G: GRB2-related adaptor protein 2
H: LAT pY226 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,6467
Polymers25,3584
Non-polymers2883
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4660 Å2
ΔGint-72 kcal/mol
Surface area10390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.637, 117.937, 50.594
Angle α, β, γ (deg.)90.00, 108.92, 90.00
Int Tables number4
Space group name H-MP1211

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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: 11823.300 Da / Num. of mol.: 4 / Fragment: Gads-SH2 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: GADS / Production host: Escherichia coli (E. coli) / References: UniProt: O89100
#2: Protein/peptide
LAT pY226 peptide


Mass: 855.783 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: THE PEPTIDE WAS CHEMICALLY SYNTHESIZED
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 441 / 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: 2.82 Å3/Da / Density % sol: 56.34 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 8.5
Details: 0.1mM Tris-HCl, 2.5M ammonium sulfate, pH 8.5, VAPOR DIFFUSION, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Apr 20, 2003 / Details: osmic mirrors
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.84→52.3 Å / Num. all: 133713 / Num. obs: 41324 / % possible obs: 92.72 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
CrystalClear(MSC/RIGAKU)data reduction
d*TREKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→30 Å / Cor.coef. Fo:Fc: 0.916 / Cor.coef. Fo:Fc free: 0.847 / SU B: 5.318 / SU ML: 0.157 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.195 / ESU R Free: 0.2 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.25855 2073 5.1 %RANDOM
Rwork0.21336 ---
all0.21745 38882 --
obs0.21745 38882 92.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 30.642 Å2
Baniso -1Baniso -2Baniso -3
1--1.15 Å20 Å2-0.76 Å2
2--1.31 Å20 Å2
3----0.65 Å2
Refinement stepCycle: LAST / Resolution: 1.9→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3533 0 35 441 4009
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0370.0213656
X-RAY DIFFRACTIONr_bond_other_d0.0030.023098
X-RAY DIFFRACTIONr_angle_refined_deg2.8831.9464925
X-RAY DIFFRACTIONr_angle_other_deg1.35337227
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.7985407
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_chiral_restr0.2020.2490
X-RAY DIFFRACTIONr_gen_planes_refined0.0170.023988
X-RAY DIFFRACTIONr_gen_planes_other0.0120.02816
X-RAY DIFFRACTIONr_nbd_refined0.2420.2804
X-RAY DIFFRACTIONr_nbd_other0.2740.24036
X-RAY DIFFRACTIONr_nbtor_other0.1030.22136
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2250.2275
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2820.214
X-RAY DIFFRACTIONr_symmetry_vdw_other0.290.251
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2220.214
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it1.7791.52084
X-RAY DIFFRACTIONr_mcangle_it2.68723361
X-RAY DIFFRACTIONr_scbond_it4.21131572
X-RAY DIFFRACTIONr_scangle_it5.7564.51564
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.337 113
Rwork0.265 1937

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