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- PDB-4lnp: The first SH3 domain from CAP/Ponsin in complex with proline rich... -

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Basic information

Entry
Database: PDB / ID: 4lnp
TitleThe first SH3 domain from CAP/Ponsin in complex with proline rich peptide from Vinculin
Components
  • Sorbin and SH3 domain-containing protein 1
  • Vinculin
KeywordsSIGNALING PROTEIN / sh3 domain / cell migration / proline rich peptide / focal adhesion
Function / homology
Function and homology information


regulation of protein localization to adherens junction / podosome ring / outer dense plaque of desmosome / inner dense plaque of desmosome / cell-substrate junction / terminal web / epithelial cell-cell adhesion / zonula adherens / dystroglycan binding / alpha-catenin binding ...regulation of protein localization to adherens junction / podosome ring / outer dense plaque of desmosome / inner dense plaque of desmosome / cell-substrate junction / terminal web / epithelial cell-cell adhesion / zonula adherens / dystroglycan binding / alpha-catenin binding / flotillin complex / fascia adherens / cell-cell contact zone / costamere / apical junction assembly / regulation of establishment of endothelial barrier / adherens junction assembly / focal adhesion assembly / axon extension / protein localization to cell surface / lamellipodium assembly / regulation of focal adhesion assembly / maintenance of blood-brain barrier / stress fiber assembly / cell-substrate adhesion / brush border / Signaling by ALK fusions and activated point mutants / Smooth Muscle Contraction / positive regulation of glycogen biosynthetic process / positive regulation of lipid biosynthetic process / stress fiber / positive regulation of insulin receptor signaling pathway / cytoskeletal protein binding / cell-matrix adhesion / negative regulation of cell migration / cell projection / morphogenesis of an epithelium / positive regulation of protein localization to plasma membrane / adherens junction / positive regulation of glucose import / sarcolemma / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / insulin receptor binding / platelet aggregation / beta-catenin binding / nuclear matrix / cellular response to insulin stimulus / specific granule lumen / Signaling by RAF1 mutants / extracellular vesicle / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / cell-cell junction / Signaling by BRAF and RAF1 fusions / signaling receptor complex adaptor activity / Platelet degranulation / insulin receptor signaling pathway / actin binding / secretory granule lumen / ficolin-1-rich granule lumen / molecular adaptor activity / cytoskeleton / cell adhesion / cadherin binding / membrane raft / focal adhesion / centrosome / ubiquitin protein ligase binding / Neutrophil degranulation / structural molecule activity / protein-containing complex / extracellular exosome / extracellular region / nucleus / plasma membrane / cytosol / cytoplasm
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 / Vinculin repeated domain signature. / Vinculin / Vinculin, conserved site ...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 / Vinculin repeated domain signature. / Vinculin / Vinculin, conserved site / Vinculin family talin-binding region signature. / Vinculin/alpha-catenin / Vinculin family / Alpha-catenin/vinculin-like superfamily / Variant SH3 domain / Variant SH3 domain / SH3 Domains / SH3 domain / Src homology 3 domains / SH3 type barrels. / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Roll / Mainly Beta
Similarity search - Domain/homology
Vinculin / Sorbin and SH3 domain-containing protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.41 Å
AuthorsZhao, D. / Li, F. / Wu, J. / Shi, Y. / Zhang, Z. / Gong, Q.
CitationJournal: J.Struct.Biol. / Year: 2014
Title: Structural investigation of the interaction between the tandem SH3 domains of c-Cbl-associated protein and vinculin
Authors: Zhao, D. / Wang, X. / Peng, J. / Wang, C. / Li, F. / Sun, Q. / Zhang, Y. / Zhang, J. / Cai, G. / Zuo, X. / Wu, J. / Shi, Y. / Zhang, Z. / Gong, Q.
History
DepositionJul 11, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 28, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 4, 2014Group: Derived calculations
Revision 1.2Dec 10, 2014Group: Database references
Revision 1.3Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Sorbin and SH3 domain-containing protein 1
B: Vinculin


Theoretical massNumber of molelcules
Total (without water)8,3412
Polymers8,3412
Non-polymers00
Water1,49583
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area930 Å2
ΔGint-4 kcal/mol
Surface area5160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)24.480, 49.850, 58.940
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 Sorbin and SH3 domain-containing protein 1 / Ponsin / SH3 domain protein 5 / SH3P12 / c-Cbl-associated protein / CAP


Mass: 7257.308 Da / Num. of mol.: 1
Fragment: protein-protein binding domain, UNP residues 794-854
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KIAA0894, KIAA1296, SH3D5, SORBS1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9BX66
#2: Protein/peptide Vinculin / / Metavinculin / MV


Mass: 1083.257 Da / Num. of mol.: 1 / Fragment: proline rich peptide, UNP residues 870-879
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: VCL / Production host: Escherichia coli (E. coli) / References: UniProt: P18206
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 83 / 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: 2.16 Å3/Da / Density % sol: 42.95 %
Crystal growTemperature: 293 K / Method: evaporation / pH: 8 / Details: pH 8.0, EVAPORATION, temperature 293K

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U
DetectorType: ADSC QUANTUM 315r / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.41→38.06 Å / Num. all: 14294 / Num. obs: 13539

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
REFMAC5.7.0032refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.41→38.06 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.955 / SU B: 2.613 / SU ML: 0.045 / Cross valid method: THROUGHOUT / ESU R: 0.063 / ESU R Free: 0.064 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19361 711 5 %RANDOM
Rwork0.13669 ---
obs0.13954 13539 98.01 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.041 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å20 Å2-0 Å2
2---0.17 Å2-0 Å2
3---0.11 Å2
Refinement stepCycle: LAST / Resolution: 1.41→38.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms587 0 0 83 670
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.019661
X-RAY DIFFRACTIONr_bond_other_d0.0010.02640
X-RAY DIFFRACTIONr_angle_refined_deg2.3942.002907
X-RAY DIFFRACTIONr_angle_other_deg1.04931493
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.891581
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.16423.14335
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.61715114
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.52157
X-RAY DIFFRACTIONr_chiral_restr0.160.290
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.022738
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02149
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_it1.8410.986298
X-RAY DIFFRACTIONr_mcbond_other1.8180.979296
X-RAY DIFFRACTIONr_mcangle_it2.1461.476372
X-RAY DIFFRACTIONr_mcangle_other2.1541.48373
X-RAY DIFFRACTIONr_scbond_it6.51.297363
X-RAY DIFFRACTIONr_scbond_other6.4211.282359
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.5131.83528
X-RAY DIFFRACTIONr_long_range_B_refined5.1569.728743
X-RAY DIFFRACTIONr_long_range_B_other4.8498.972706
X-RAY DIFFRACTIONr_rigid_bond_restr4.76331301
X-RAY DIFFRACTIONr_sphericity_free41.807518
X-RAY DIFFRACTIONr_sphericity_bonded18.39951340
LS refinement shellResolution: 1.41→1.447 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.298 40 -
Rwork0.2 892 -
obs--85.5 %

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