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- PDB-2w10: Mona SH3C in complex -

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Basic information

Entry
Database: PDB / ID: 2w10
TitleMona SH3C in complex
Components
  • GRB2-RELATED ADAPTOR PROTEIN 2
  • TYROSINE-PROTEIN PHOSPHATASE NON-RECEPTOR TYPE 23
KeywordsHYDROLASE / ALTERNATIVE SPLICING / TPR REPEAT / SH2 DOMAIN / SH3 DOMAIN / COILED COIL / PROTEIN PHOSPHATASE / CYTOPLASMIC VESICLE / PHOSPHOPROTEIN / SIGNAL TRANDUCTION / SH3 DOMAIN-COMPLEX / SH3 / GADS / MONA / DIMER / HD-PTP / CYTOPLASM
Function / homology
Function and homology information


positive regulation of adherens junction organization / positive regulation of homophilic cell adhesion / FLT3 Signaling / CD28 co-stimulation / FCERI mediated MAPK activation / positive regulation of Wnt protein secretion / Signaling by SCF-KIT / Generation of second messenger molecules / positive regulation of early endosome to late endosome transport / FCERI mediated Ca+2 mobilization ...positive regulation of adherens junction organization / positive regulation of homophilic cell adhesion / FLT3 Signaling / CD28 co-stimulation / FCERI mediated MAPK activation / positive regulation of Wnt protein secretion / Signaling by SCF-KIT / Generation of second messenger molecules / positive regulation of early endosome to late endosome transport / FCERI mediated Ca+2 mobilization / negative regulation of epithelial cell migration / early endosome to late endosome transport / ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / endocytic recycling / DAP12 signaling / regulation of MAPK cascade / cilium assembly / phosphotyrosine residue binding / protein-tyrosine-phosphatase / ciliary basal body / protein tyrosine phosphatase activity / protein transport / nuclear body / early endosome / endosome / protein kinase binding / signal transduction / nucleoplasm / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
GRAP2, C-terminal SH3 domain / ALIX V-shaped domain / ALIX V-shaped domain binding to HIV / BRO1 domain / BRO1 domain superfamily / BRO1-like domain / BRO1 domain profile. / BRO1-like domain / Grb2-like / SH3 Domains ...GRAP2, C-terminal SH3 domain / ALIX V-shaped domain / ALIX V-shaped domain binding to HIV / BRO1 domain / BRO1 domain superfamily / BRO1-like domain / BRO1 domain profile. / BRO1-like domain / Grb2-like / SH3 Domains / Protein tyrosine phosphatase, catalytic domain / PTP type protein phosphatase domain profile. / Protein-tyrosine phosphatase / Tyrosine-specific protein phosphatase, PTPase domain / Protein-tyrosine phosphatase, catalytic / Protein tyrosine phosphatase, catalytic domain motif / Tyrosine specific protein phosphatases active site. / Protein-tyrosine phosphatase, active site / Tyrosine-specific protein phosphatases domain / Tyrosine specific protein phosphatases domain profile. / Protein-tyrosine phosphatase-like / 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 / Mainly Beta
Similarity search - Domain/homology
PHOSPHATE ION / GRB2-related adaptor protein 2 / Tyrosine-protein phosphatase non-receptor type 23
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsHarkiolaki, M. / Feller, S.M.
CitationJournal: Structure / Year: 2009
Title: Distinct Binding Modes of Two Epitopes in Gab2 that Interact with the Sh3C Domain of Grb2.
Authors: Harkiolaki, M. / Tsirka, T. / Lewitzky, M. / Simister, P.C. / Joshi, D. / Bird, L.E. / Jones, E.Y. / O'Reilly, N. / Feller, S.M.
History
DepositionOct 13, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 19, 2009Provider: 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 / Derived calculations / 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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: TYROSINE-PROTEIN PHOSPHATASE NON-RECEPTOR TYPE 23
D: TYROSINE-PROTEIN PHOSPHATASE NON-RECEPTOR TYPE 23
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,9396
Polymers16,7494
Non-polymers1902
Water2,432135
1
A: GRB2-RELATED ADAPTOR PROTEIN 2
D: TYROSINE-PROTEIN PHOSPHATASE NON-RECEPTOR TYPE 23
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,4703
Polymers8,3752
Non-polymers951
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1420 Å2
ΔGint-10.5 kcal/mol
Surface area5830 Å2
MethodPQS
2
B: GRB2-RELATED ADAPTOR PROTEIN 2
C: TYROSINE-PROTEIN PHOSPHATASE NON-RECEPTOR TYPE 23
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,4703
Polymers8,3752
Non-polymers951
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1180 Å2
ΔGint-5.5 kcal/mol
Surface area5730 Å2
MethodPQS
Unit cell
Length a, b, c (Å)26.137, 34.367, 36.220
Angle α, β, γ (deg.)81.08, 87.05, 72.55
Int Tables number1
Space group name H-MP1

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Components

#1: Protein GRB2-RELATED ADAPTOR PROTEIN 2 / MONA SH3C / GADS PROTEIN / GROWTH FACTOR RECEPTOR BINDING PROTEIN / GRB-2-LIKE PROTEIN / GRB2L / ...MONA SH3C / 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: 7088.970 Da / Num. of mol.: 2 / Fragment: SH3 2, RESIDUES 265-322
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: O89100
#2: Protein/peptide TYROSINE-PROTEIN PHOSPHATASE NON-RECEPTOR TYPE 23 / HD-PTP


Mass: 1285.575 Da / Num. of mol.: 2 / Fragment: SH3 BINDING REGION, RESIDUES 719-730 / Source method: obtained synthetically / Source: (synth.) MUS MUSCULUS (house mouse) / References: UniProt: Q6PB44, protein-tyrosine-phosphatase
#3: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 135 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsPLGS OVERHANG DUE TO EXPRESSION VECTOR

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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: 1.67 Å3/Da / Density % sol: 25.96 % / Description: NONE
Crystal growpH: 7.5
Details: 0.1 M PHOSPHATE CITRATE, 2 M AMMONIUM SULPHATE, pH 7.5

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.978
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 15, 2006 / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 1.86→30 Å / Num. obs: 8966 / % possible obs: 81.9 % / Observed criterion σ(I): 1 / Redundancy: 2 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 18.7
Reflection shellResolution: 1.86→1.94 Å / Redundancy: 2 % / Rmerge(I) obs: 0.06 / Mean I/σ(I) obs: 11.5 / % possible all: 44.2

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Processing

Software
NameVersionClassification
REFMAC5.5.0047refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1UTI

1uti


Resolution: 1.9→35.78 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.887 / SU B: 3.927 / SU ML: 0.117 / Cross valid method: THROUGHOUT / ESU R: 0.197 / ESU R Free: 0.177 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.231 425 4.7 %RANDOM
Rwork0.161 ---
obs0.164 8539 96.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 12.28 Å2
Baniso -1Baniso -2Baniso -3
1--0.55 Å20.31 Å20.13 Å2
2--0.23 Å2-0.29 Å2
3---0.21 Å2
Refinement stepCycle: LAST / Resolution: 1.9→35.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1146 0 10 135 1291
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0221205
X-RAY DIFFRACTIONr_bond_other_d0.0050.02864
X-RAY DIFFRACTIONr_angle_refined_deg1.6441.9791646
X-RAY DIFFRACTIONr_angle_other_deg0.93532079
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5785144
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.69422.22254
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.25915178
X-RAY DIFFRACTIONr_dihedral_angle_4_deg26.0061512
X-RAY DIFFRACTIONr_chiral_restr0.0890.2168
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211312
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02254
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8121.5731
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.45121177
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.5123474
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.6254.5467
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: 1.9→1.95 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.209 22
Rwork0.163 587

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