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- PDB-1r1q: Structural Basis for Differential Recognition of Tyrosine Phospho... -

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Basic information

Entry
Database: PDB / ID: 1r1q
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 pY191 peptide
KeywordsPEPTIDE BINDING PROTEIN / SH2 / Gads / LAT / phosphopeptide
Function / homology
Function and homology information


FLT3 Signaling / Co-stimulation by CD28 / FCERI mediated MAPK activation / Signaling by SCF-KIT / Generation of second messenger molecules / FCERI mediated Ca+2 mobilization / DAP12 signaling / endosome / nucleoplasm / nucleus ...FLT3 Signaling / Co-stimulation by CD28 / FCERI mediated MAPK activation / Signaling by SCF-KIT / Generation of second messenger molecules / FCERI mediated Ca+2 mobilization / DAP12 signaling / endosome / nucleoplasm / nucleus / plasma membrane / cytoplasm / cytosol
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: 1.8 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
Revision 1.4Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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: GRB2-related adaptor protein 2
C: LAT pY191 peptide
D: LAT pY191 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,8038
Polymers25,4184
Non-polymers3844
Water2,558142
1
A: GRB2-related adaptor protein 2
C: LAT pY191 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,8053
Polymers12,7092
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1470 Å2
ΔGint-35 kcal/mol
Surface area6360 Å2
MethodPISA
2
B: GRB2-related adaptor protein 2
D: LAT pY191 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,9975
Polymers12,7092
Non-polymers2883
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1440 Å2
ΔGint-37 kcal/mol
Surface area6460 Å2
MethodPISA
3
B: GRB2-related adaptor protein 2
D: LAT pY191 peptide
hetero molecules

A: GRB2-related adaptor protein 2
C: LAT pY191 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,8038
Polymers25,4184
Non-polymers3844
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y+1/2,-z+11
Buried area5070 Å2
ΔGint-94 kcal/mol
Surface area10660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.710, 51.810, 43.970
Angle α, β, γ (deg.)90.00, 101.38, 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.: 2 / 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 pY191 peptide


Mass: 885.878 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: THE PEPTIDE WAS CHEMICALLY SYNTHESIZED
#3: Chemical
ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 142 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 1.88 Å3/Da / Density % sol: 34.43 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 8.7
Details: 0.1mM Tris-HCl, 2.5M ammonium sulfate, pH 8.7, 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 23, 2003 / Details: mirrors
RadiationMonochromator: osmic mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.62→43.1 Å / Num. all: 117803 / Num. obs: 26632 / % possible obs: 96.6 % / 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: 1.8→43.03 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.939 / SU B: 3.007 / SU ML: 0.093 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.155 / ESU R Free: 0.143 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2253 911 5.2 %RANDOM
Rwork0.17649 ---
all0.17906 16497 --
obs0.17906 16497 99.07 %-
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: 21.308 Å2
Baniso -1Baniso -2Baniso -3
1-0.65 Å20 Å2-0.25 Å2
2---0.09 Å20 Å2
3----0.66 Å2
Refinement stepCycle: LAST / Resolution: 1.8→43.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1811 0 20 142 1973
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0211875
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9241.9442528
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9345212
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_chiral_restr0.150.2252
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021443
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1980.2850
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1470.2131
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1930.274
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1950.219
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it1.2441.51069
X-RAY DIFFRACTIONr_mcangle_it2.02821730
X-RAY DIFFRACTIONr_scbond_it3.193806
X-RAY DIFFRACTIONr_scangle_it4.8144.5798
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.363 59
Rwork0.291 1216

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