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- PDB-2o9v: The second SH3 domain from Ponsin in complex with the paxillin pr... -

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Basic information

Entry
Database: PDB / ID: 2o9v
TitleThe second SH3 domain from Ponsin in complex with the paxillin proline rich region
Components
  • Paxillin
  • Ponsin
KeywordsSIGNALING PROTEIN/CELL ADHESION / SH3 DOMAIN / PONSIN / Paxillin / proline-rich-region / SIGNALING PROTEIN-CELL ADHESION COMPLEX
Function / homology
Function and homology information


Regulation of cytoskeletal remodeling and cell spreading by IPP complex components / Localization of the PINCH-ILK-PARVIN complex to focal adhesions / cell-substrate junction / zonula adherens / Regulation of MITF-M-dependent genes involved in extracellular matrix, focal adhesion and epithelial-to-mesenchymal transition / neuropilin binding / flotillin complex / vinculin binding / focal adhesion assembly / signal complex assembly ...Regulation of cytoskeletal remodeling and cell spreading by IPP complex components / Localization of the PINCH-ILK-PARVIN complex to focal adhesions / cell-substrate junction / zonula adherens / Regulation of MITF-M-dependent genes involved in extracellular matrix, focal adhesion and epithelial-to-mesenchymal transition / neuropilin binding / flotillin complex / vinculin binding / focal adhesion assembly / signal complex assembly / microtubule associated complex / growth hormone receptor signaling pathway / stress fiber assembly / cell-substrate adhesion / Smooth Muscle Contraction / positive regulation of insulin receptor signaling pathway / positive regulation of glycogen biosynthetic process / GAB1 signalosome / endothelial cell migration / positive regulation of lipid biosynthetic process / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / cytoskeletal protein binding / stress fiber / positive regulation of stress fiber assembly / substrate adhesion-dependent cell spreading / transforming growth factor beta receptor signaling pathway / cell-matrix adhesion / positive regulation of D-glucose import / cellular response to reactive oxygen species / insulin receptor binding / positive regulation of protein localization to plasma membrane / adherens junction / beta-catenin binding / VEGFA-VEGFR2 Pathway / nuclear matrix / cellular response to insulin stimulus / cell-cell junction / insulin receptor signaling pathway / cell migration / lamellipodium / signaling receptor complex adaptor activity / actin binding / cell cortex / protein phosphatase binding / cell adhesion / membrane raft / focal adhesion / centrosome / signal transduction / metal ion binding / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
c-Cbl associated protein, SH3 domain / c-Cbl associated protein, SH3 domain 1 / c-Cbl associated protein, SH3 domain 2 / SoHo domain / Sorbin homologous domain / SoHo domain profile. / Sorbin homologous domain / Paxillin / : / : ...c-Cbl associated protein, SH3 domain / c-Cbl associated protein, SH3 domain 1 / c-Cbl associated protein, SH3 domain 2 / SoHo domain / Sorbin homologous domain / SoHo domain profile. / Sorbin homologous domain / Paxillin / : / : / Paxillin family / : / LIM zinc-binding domain signature. / LIM domain / Zinc-binding domain present in Lin-11, Isl-1, Mec-3. / Zinc finger, LIM-type / LIM domain profile. / Variant SH3 domain / Variant SH3 domain / SH3 Domains / SH3 domain / SH3 type barrels. / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Roll / Mainly Beta
Similarity search - Domain/homology
Sorbin and SH3 domain-containing protein 1 / Paxillin / Sorbin and SH3 domain-containing protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.63 Å
AuthorsPinotsis, N. / Wilmanns, M.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Paxillin and ponsin interact in nascent costameres of muscle cells
Authors: Gehmlich, K. / Pinotsis, N. / Hayess, K. / van der Ven, P.F. / Milting, H. / El Banayosy, A. / Wilmanns, M. / Ehler, E.
History
DepositionDec 14, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 30, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 18, 2017Group: Refinement description / Category: software / Item: _software.name
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 / diffrn_source / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ponsin
B: Paxillin


Theoretical massNumber of molelcules
Total (without water)8,6822
Polymers8,6822
Non-polymers00
Water1,67593
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)24.490, 41.852, 58.790
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Ponsin


Mass: 7698.707 Da / Num. of mol.: 1 / Fragment: SRC HOMOLOGY 3 (SH3) DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SORBS1 / Plasmid: PET151 / Production host: Escherichia coli (E. coli) / References: UniProt: A0AED4, UniProt: Q9BX66*PLUS
#2: Protein/peptide Paxillin


Mass: 983.158 Da / Num. of mol.: 1 / Fragment: Proline rich region / Source method: obtained synthetically
Details: The peptide was chemically synthesized. The sequence of the peptide is naturally found in Homo sapiens (human)
References: UniProt: P49023
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 93 / 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: 1.74 Å3/Da / Density % sol: 29.11 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2M Sodium Acetate, 0.1M Sodium Cacodylate, 30% (w/v) PEG 8000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.8156 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jun 1, 2006
RadiationMonochromator: Ge Single Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8156 Å / Relative weight: 1
ReflectionResolution: 1.63→25 Å / Num. all: 8022 / Num. obs: 7747 / % possible obs: 96.6 % / Redundancy: 5 % / Biso Wilson estimate: 17.1 Å2 / Rmerge(I) obs: 0.059 / Net I/σ(I): 24
Reflection shellResolution: 1.63→1.66 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.221 / Mean I/σ(I) obs: 4.2 / Num. unique all: 380 / % possible all: 80.5

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MAR345data collection
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2O2W

2o2w


Resolution: 1.63→18.81 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.964 / SU B: 3.481 / SU ML: 0.058 / Cross valid method: THROUGHOUT / ESU R: 0.181 / ESU R Free: 0.092 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.17686 218 2.8 %RANDOM
Rwork0.14255 ---
obs0.1436 7500 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 18.46 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å20 Å20 Å2
2--0.03 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.63→18.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms651 0 0 97 748
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.022673
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6081.982922
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.878583
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.44922.532
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.19615107
X-RAY DIFFRACTIONr_dihedral_angle_4_deg29.795158
X-RAY DIFFRACTIONr_chiral_restr0.1060.296
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02545
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2140.2286
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3220.2470
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1750.276
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.310.273
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2910.220
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.1931.5420
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.422685
X-RAY DIFFRACTIONr_scbond_it4.623279
X-RAY DIFFRACTIONr_scangle_it6.7464.5237
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.63→1.672 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.24 17 -
Rwork0.214 450 -
obs--100 %

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