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- PDB-5ob0: Crystal structure of the c-Src-SH3 domain Q128E mutant in complex... -

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Basic information

Entry
Database: PDB / ID: 5ob0
TitleCrystal structure of the c-Src-SH3 domain Q128E mutant in complex with the high affinity peptide APP12
Components
  • APP12
  • Proto-oncogene tyrosine-protein kinase Src
KeywordsTRANSFERASE / beta shandwich
Function / homology
Function and homology information


Signaling by ERBB2 / Nuclear signaling by ERBB4 / Signaling by SCF-KIT / Regulation of KIT signaling / Signaling by EGFR / GAB1 signalosome / Regulation of gap junction activity / FCGR activation / PECAM1 interactions / Co-stimulation by CD28 ...Signaling by ERBB2 / Nuclear signaling by ERBB4 / Signaling by SCF-KIT / Regulation of KIT signaling / Signaling by EGFR / GAB1 signalosome / Regulation of gap junction activity / FCGR activation / PECAM1 interactions / Co-stimulation by CD28 / Co-inhibition by CTLA4 / EPHA-mediated growth cone collapse / Ephrin signaling / G alpha (i) signalling events / GP1b-IX-V activation signalling / Thrombin signalling through proteinase activated receptors (PARs) / VEGFR2 mediated cell proliferation / RET signaling / Receptor Mediated Mitophagy / ADP signalling through P2Y purinoceptor 1 / RAF activation / PIP3 activates AKT signaling / EPH-ephrin mediated repulsion of cells / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / Activated NTRK3 signals through PI3K / Downstream signal transduction / Downregulation of ERBB4 signaling / Cyclin D associated events in G1 / Regulation of RUNX3 expression and activity / MAP2K and MAPK activation / Integrin signaling / GRB2:SOS provides linkage to MAPK signaling for Integrins / DCC mediated attractive signaling / MET activates PTK2 signaling / Extra-nuclear estrogen signaling / EPHB-mediated forward signaling / p130Cas linkage to MAPK signaling for integrins / VEGFA-VEGFR2 Pathway / connexin binding / negative regulation of intrinsic apoptotic signaling pathway / immune system process / progesterone receptor signaling pathway / negative regulation of extrinsic apoptotic signaling pathway / non-membrane spanning protein tyrosine kinase activity / non-specific protein-tyrosine kinase / epidermal growth factor receptor signaling pathway / cell junction / cell-cell junction / protein tyrosine kinase activity / protein phosphatase binding / cell differentiation / cytoskeleton / mitochondrial inner membrane / regulation of cell cycle / cell adhesion / endosome membrane / signaling receptor binding / focal adhesion / heme binding / perinuclear region of cytoplasm / protein-containing complex / ATP binding / nucleus / membrane / plasma membrane / cytosol
Similarity search - Function
SH3 Domains / : / SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / SH2 domain superfamily / Src homology 3 domains / SH3 type barrels. ...SH3 Domains / : / SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / SH2 domain superfamily / Src homology 3 domains / SH3 type barrels. / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / Tyrosine-protein kinase, active site / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Roll / 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
Proto-oncogene tyrosine-protein kinase Src
Similarity search - Component
Biological speciesGallus gallus (chicken)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.172 Å
AuthorsCamara-Artigas, A.
Funding support Spain, 1items
OrganizationGrant numberCountry
Spanish Ministry of Economy and CompetitivenessBIO2016-78020-R Spain
CitationJournal: to be published
Title: Crystal structure of the c-Src-SH3 domain Q128E mutant in complex with the high affinity peptide APP12
Authors: Camara-Artigas, A.
History
DepositionJun 25, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 12, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Jan 24, 2018Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain
Revision 1.3Feb 20, 2019Group: Data collection / Source and taxonomy / Category: database_PDB_remark / pdbx_entity_src_syn
Item: _database_PDB_remark.text / _pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_scientific
Revision 1.4Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Proto-oncogene tyrosine-protein kinase Src
B: APP12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,4153
Polymers8,3192
Non-polymers961
Water1,69394
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: light scattering, Complex of the SH3 domain with the proline rich synthetic peptide APP12
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1310 Å2
ΔGint-13 kcal/mol
Surface area4680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)31.630, 32.560, 65.262
Angle α, β, γ (deg.)90.000, 103.020, 90.000
Int Tables number5
Space group name H-MI121
Components on special symmetry positions
IDModelComponents
11A-93-

GLU

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Components

#1: Protein Proto-oncogene tyrosine-protein kinase Src / Proto-oncogene c-Src / pp60c-src / p60-Src


Mass: 6906.483 Da / Num. of mol.: 1 / Fragment: SH3 DOMAIN / Mutation: Q128E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: SRC / Plasmid: pET15b / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P00523, non-specific protein-tyrosine kinase
#2: Protein/peptide APP12


Mass: 1412.705 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 94 / 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: 2.07 Å3/Da / Density % sol: 40.6 % / Mosaicity: 1.09 °
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 1.9 M Ammonium sulphate, 0.05 M sodium chloride, 0.1 M sodium acetate and 10% Glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9334 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 24, 2013
Details: vertical focusing mirror (VFM) and a horizontal focusing mirror(HFM), manufactured by IRELEC.
RadiationMonochromator: Si(111) channel-cut crystal monochromator and a pair of KB mirrors
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9334 Å / Relative weight: 1
ReflectionResolution: 1.17→25 Å / Num. obs: 41471 / % possible obs: 97.3 % / Redundancy: 2.6 % / Biso Wilson estimate: 7.36 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.074 / Rpim(I) all: 0.053 / Rrim(I) all: 0.091 / Net I/σ(I): 6.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Rpim(I) allRrim(I) all% possible all
1.17-1.192.10.1660.9360.1270.2194.6
6.42-25.562.40.0460.9890.0320.05656.4

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Processing

Software
NameVersionClassification
Aimless0.3.11data scaling
PHENIXrefinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ZJ4

4zj4
PDB Unreleased entry


Resolution: 1.172→25 Å / SU ML: 0.08 / Cross valid method: THROUGHOUT / σ(F): 0.78 / Phase error: 13.2
RfactorNum. reflection% reflection
Rfree0.1491 2051 4.95 %
Rwork0.1311 --
obs0.132 41471 97.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 35.28 Å2 / Biso mean: 11.1835 Å2 / Biso min: 4.28 Å2
Refinement stepCycle: final / Resolution: 1.172→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms561 0 5 94 660
Biso mean--20.74 21.11 -
Num. residues----70
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009599
X-RAY DIFFRACTIONf_angle_d1.164824
X-RAY DIFFRACTIONf_chiral_restr0.08187
X-RAY DIFFRACTIONf_plane_restr0.01110
X-RAY DIFFRACTIONf_dihedral_angle_d16.31222
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.172-1.19930.211270.16922586271395
1.1993-1.22930.19441460.14792667281399
1.2293-1.26250.1411270.13362685281299
1.2625-1.29970.17271530.13422621277498
1.2997-1.34160.19171310.13192679281099
1.3416-1.38950.16231460.12952647279399
1.3895-1.44520.14021430.12522655279899
1.4452-1.51090.15841400.12192706284699
1.5109-1.59060.14991390.11452644278399
1.5906-1.69020.14651330.11152666279999
1.6902-1.82070.15681070.11972693280098
1.8207-2.00390.13261430.11792612275598
2.0039-2.29370.09651410.112617275897
2.2937-2.88910.13921340.13912623275798
2.8891-25.56990.17191410.15852319246086

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