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- PDB-1uti: Mona/Gads SH3C in complex with HPK derived peptide -

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Basic information

Entry
Database: PDB / ID: 1uti
TitleMona/Gads SH3C in complex with HPK derived peptide
Components
  • GRB2-RELATED ADAPTOR PROTEIN 2
  • MITOGEN-ACTIVATED PROTEIN KINASE KINASE KINASE KINASE 1
KeywordsSIGNALING PROTEIN REGULATOR / SH3 DOMAIN-COMPLEX / ADAPTOR PROTEIN (MONA) / PROTEIN SERINE/THREONINE KINASE (HPK1) / ANTIGEN RECEPTOR SIGNALLING MEDIATOR (BOTH) / SH3 DOMAIN / PPII HELIX
Function / homology
Function and homology information


: / FLT3 Signaling / CD28 co-stimulation / FCERI mediated MAPK activation / Signaling by SCF-KIT / MAP kinase kinase kinase kinase activity / Generation of second messenger molecules / FCERI mediated Ca+2 mobilization / cellular response to phorbol 13-acetate 12-myristate / DAP12 signaling ...: / FLT3 Signaling / CD28 co-stimulation / FCERI mediated MAPK activation / Signaling by SCF-KIT / MAP kinase kinase kinase kinase activity / Generation of second messenger molecules / FCERI mediated Ca+2 mobilization / cellular response to phorbol 13-acetate 12-myristate / DAP12 signaling / regulation of MAPK cascade / phosphotyrosine residue binding / peptidyl-serine phosphorylation / cell population proliferation / protein autophosphorylation / non-specific serine/threonine protein kinase / endosome / intracellular signal transduction / protein phosphorylation / protein serine/threonine kinase activity / signal transduction / nucleoplasm / ATP binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
GRAP2, C-terminal SH3 domain / Mitogen-activated protein (MAP) kinase kinase kinase kinase / Domain found in NIK1-like kinases, mouse citron and yeast ROM1, ROM2 / Citron homology (CNH) domain / CNH domain / Citron homology (CNH) domain profile. / Grb2-like / SH3 Domains / SH3 domain / SH2 domain ...GRAP2, C-terminal SH3 domain / Mitogen-activated protein (MAP) kinase kinase kinase kinase / Domain found in NIK1-like kinases, mouse citron and yeast ROM1, ROM2 / Citron homology (CNH) domain / CNH domain / Citron homology (CNH) domain profile. / Grb2-like / SH3 Domains / SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / Src homology 3 domains / SH3 type barrels. / SH2 domain superfamily / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Roll / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Mainly Beta
Similarity search - Domain/homology
GRB2-related adaptor protein 2 / Mitogen-activated protein kinase kinase kinase kinase 1
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsLewitzky, M. / Harkiolaki, M. / Domart, M.C. / Feller, S.M.
CitationJournal: J.Biol.Chem. / Year: 2004
Title: Mona/Gads Sh3C Binding to Hematopoietic Progenitor Kinase 1 (Hpk1) Combines an Atypical SH3 Binding Motif, R/Kxxk, with a Classical Pxxp Motif Embedded in a Polyproline Type II (Ppii) Helix
Authors: Lewitzky, M. / Harkiolaki, M. / Domart, M.C. / Jones, E. / Feller, S.M.
History
DepositionDec 9, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 6, 2004Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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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
D: MITOGEN-ACTIVATED PROTEIN KINASE KINASE KINASE KINASE 1


Theoretical massNumber of molelcules
Total (without water)8,5582
Polymers8,5582
Non-polymers00
Water1,13563
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)71.456, 27.442, 33.043
Angle α, β, γ (deg.)90.00, 104.22, 90.00
Int Tables number5
Space group name H-MC121
DetailsMONA/GADS SH3C IS A MONOMER IN SOLUTION, PRESENT IN THISCRYSTAL IN COMPLEX WITH AN HPK1 DERIVED PEPTIDE AND HENCEIN A HETERODIMERIC STATE.

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Components

#1: Protein GRB2-RELATED ADAPTOR PROTEIN 2 / GADS PROTEIN / GROWTH FACTOR RECEPTOR BINDING PROTEIN / GRB-2-LIKE PROTEIN / GRB2L / HEMATOPOIETIC ...GADS PROTEIN / GROWTH FACTOR RECEPTOR BINDING PROTEIN / GRB-2-LIKE PROTEIN / GRB2L / HEMATOPOIETIC CELL-ASSOCIATED ADAPTOR PROTEIN GRPL / GRB-2-RELATED MONOCYTIC ADAPTER PROTEIN / MONOCYTIC ADAPTER / MONA / ADAPTER PROTEIN GRID


Mass: 6734.568 Da / Num. of mol.: 1 / Fragment: SH3C DOMAIN, RESIDUES 265-322
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Plasmid: PGEX-6P-1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O89100
#2: Protein/peptide MITOGEN-ACTIVATED PROTEIN KINASE KINASE KINASE KINASE 1 / HEMATOPOETIC PRGENITOR KINASE I / MAPK/ERK KINASE KINASE KINASE 1 / MEK KINASE KINASE 1 / MEKKK 1 / HPK


Mass: 1823.232 Da / Num. of mol.: 1 / Fragment: SH3 BINDING PEPTIDE, RESIDUES 465-480 / Source method: obtained synthetically / Source: (synth.) MUS MUSCULUS (house mouse) / References: UniProt: P70218, EC: 2.7.1.37
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 63 / Source method: isolated from a natural source / Formula: H2O
Compound detailsGADS/MONA:INTERACTS WITH SLP-76 TO REGULATE NF-AT ACTIVATION.
Sequence detailsONLY THE C-TERMINAL DOMAIN HAS BEEN CRYSTALLISED

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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: 1.8 Å3/Da / Density % sol: 32.7 %
Crystal growpH: 7.5 / Details: 2M AMMONIUM SULFATE, 0.05M HEPES PH7.5, pH 7.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.97932
DetectorType: MARRESEARCH / Detector: CCD / Date: Aug 15, 2003 / Details: MIRRORS
RadiationMonochromator: SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97932 Å / Relative weight: 1
ReflectionResolution: 1.5→20 Å / Num. obs: 9855 / % possible obs: 97.4 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.03 / Net I/σ(I): 25.2
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 3 % / Rmerge(I) obs: 0.065 / Mean I/σ(I) obs: 14.7 / % possible all: 98.2

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1OEB

1oeb


Resolution: 1.5→34.71 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.94 / SU B: 1.308 / SU ML: 0.051 / Cross valid method: THROUGHOUT / ESU R: 0.098 / ESU R Free: 0.089 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.221 485 4.8 %RANDOM
Rwork0.207 ---
obs0.208 9573 99.3 %-
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: 14.04 Å2
Baniso -1Baniso -2Baniso -3
1--1.31 Å20 Å2-0.21 Å2
2--0.25 Å20 Å2
3---0.95 Å2
Refinement stepCycle: LAST / Resolution: 1.5→34.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms590 0 0 63 653
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.021619
X-RAY DIFFRACTIONr_bond_other_d0.0020.02563
X-RAY DIFFRACTIONr_angle_refined_deg1.1131.961836
X-RAY DIFFRACTIONr_angle_other_deg0.78531313
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.625571
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0740.283
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02672
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02132
X-RAY DIFFRACTIONr_nbd_refined0.190.2102
X-RAY DIFFRACTIONr_nbd_other0.2330.2662
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0810.2377
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1350.241
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0040.21
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2220.262
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1380.216
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6991.5365
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.3122587
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.593254
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.6044.5248
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.5→1.54 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.21 44
Rwork0.206 674

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