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- PDB-6xx4: Crystal structure of the c-Src SH3 domain H122R-Q128E mutant in c... -

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Basic information

Entry
Database: PDB / ID: 6xx4
TitleCrystal structure of the c-Src SH3 domain H122R-Q128E mutant in complex with Ni(II) at pH 7.5 co-crystallized with methyl beta-cyclodextrin
ComponentsProto-oncogene tyrosine-protein kinase Src
KeywordsPROTEIN BINDING / beta barrel / SH3 domain
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 / 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 / histone H3Y41 kinase activity / histone H2AXY142 kinase activity / cell differentiation / mitochondrial inner membrane / cytoskeleton / regulation of cell cycle / cell adhesion / endosome membrane / signaling receptor binding / innate immune response / 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 / Src homology 3 domains / SH3 type barrels. / SH2 domain superfamily ...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 / 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
methyl-beta-cyclodextrin / NICKEL (II) ION / Proto-oncogene tyrosine-protein kinase Src
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.05 Å
Model detailsATCUN site
AuthorsCamara-Artigas, A.
Funding support Spain, 1items
OrganizationGrant numberCountry
Spanish Ministry of Science, Innovation, and UniversitiesBIO2016-78020-R Spain
CitationJournal: J.Biol.Inorg.Chem. / Year: 2020
Title: The effect of an engineered ATCUN motif on the structure and biophysical properties of the SH3 domain of c-Src tyrosine kinase.
Authors: Plaza-Garrido, M. / Salinas-Garcia, M.C. / Martinez, J.C. / Camara-Artigas, A.
History
DepositionJan 26, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 22, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 3, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 2.0Jul 29, 2020Group: Atomic model / Author supporting evidence ...Atomic model / Author supporting evidence / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_instance_feature / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.id / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.src_method / _entity.type / _pdbx_struct_conn_angle.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _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: Proto-oncogene tyrosine-protein kinase Src
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,2353
Polymers6,9261
Non-polymers1,3102
Water66737
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area250 Å2
ΔGint-10 kcal/mol
Surface area4540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.571, 35.571, 81.128
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

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


Mass: 6925.530 Da / Num. of mol.: 1 / Mutation: H122R Q128E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: SRC / Plasmid: pHTP1 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P00523, non-specific protein-tyrosine kinase
#2: Polysaccharide Cyclic 2,3-di-O-methyl-alpha-D-glucopyranose-(1-4)-2-O-methyl-alpha-D-glucopyranose-(1-4)-2,6-di-O- ...Cyclic 2,3-di-O-methyl-alpha-D-glucopyranose-(1-4)-2-O-methyl-alpha-D-glucopyranose-(1-4)-2,6-di-O-methyl-alpha-D-glucopyranose-(1-4)-2-O-methyl-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-3-O-methyl-alpha-D-glucopyranose / methyl-beta-cyclodextrin


Type: oligosaccharide, Oligosaccharide / Class: Drug delivery / Mass: 1251.185 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: cyclic oligosaccharide / References: methyl-beta-cyclodextrin
DescriptorTypeProgram
WURCS=2.0/5,7,7/[a2122h-1a_1-5_2*OC_3*OC][a2122h-1a_1-5_3*OC][a2122h-1a_1-5][a2122h-1a_1-5_2*OC][a2122h-1a_1-5_2*OC_6*OC]/1-2-3-3-4-5-4/a1-g4_a4-b1_b4-c1_c4-d1_d4-e1_e4-f1_f4-g1WURCSPDB2Glycan 1.1.0
#3: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 37 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.14 Å3/Da / Density % sol: 42.51 % / Mosaicity: 0.11 °
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 1.4 M ammonium sulfate, 0.1 HEPES, 5 mM nickel chloride, 10% glycerol, 10mM methyl beta-cyclodextrin

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.979464 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 14, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979464 Å / Relative weight: 1
ReflectionResolution: 1.05→30.81 Å / Num. obs: 53538 / % possible obs: 99.9 % / Redundancy: 6.2 % / Biso Wilson estimate: 13.1 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.036 / Rpim(I) all: 0.016 / Rrim(I) all: 0.039 / Net I/σ(I): 25.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.05-1.075.80.487842814540.9410.2190.5353.699.9
5.65-30.814.70.0389882090.9950.020.04451.193.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.1.30data scaling
PHASERphasing
PHENIX1.17.1refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4JZ4

4jz4


Resolution: 1.05→28.799 Å / SU ML: 0.08 / Cross valid method: THROUGHOUT / σ(F): 0.24 / Phase error: 15.5
RfactorNum. reflection% reflection
Rfree0.1843 2695 5.03 %
Rwork0.166 --
obs0.1668 53538 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 48.08 Å2 / Biso mean: 18.4159 Å2 / Biso min: 10.05 Å2
Refinement stepCycle: final / Resolution: 1.05→28.799 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms427 0 169 37 633
Biso mean--21.83 25.3 -
Num. residues----55
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.05-1.06910.24041330.21962701100
1.0691-1.08970.21781620.19322631100
1.0897-1.11190.25091390.16962690100
1.1119-1.13610.16461370.15072713100
1.1361-1.16260.15931660.13192618100
1.1626-1.19160.13591310.13512693100
1.1916-1.22380.16081380.13612704100
1.2238-1.25990.15991300.13742661100
1.2599-1.30050.14771460.13032674100
1.3005-1.3470.17531240.13542691100
1.347-1.40090.16061370.12842701100
1.4009-1.46470.12971600.13532639100
1.4647-1.54190.1261510.13162726100
1.5419-1.63850.1681450.13612628100
1.6385-1.7650.17151640.14112681100
1.765-1.94260.15871380.14532655100
1.9426-2.22360.16251360.14652723100
2.2236-2.80110.19981440.19182644100
2.8011-28.7990.23271140.1989267098

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