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- PDB-5oav: High resolution crystal structure of the c-Src-SH3 domain mutant ... -

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Basic information

Entry
Database: PDB / ID: 5oav
TitleHigh resolution crystal structure of the c-Src-SH3 domain mutant E93V in complex with the high affinity synthetic peptide APP12: monoclinic crystal
Components
  • APP12
  • Proto-oncogene tyrosine-protein kinase Src
KeywordsTRANSFERASE / beta sandwich
Function / homology
Function and homology information


Signaling by ERBB2 / Nuclear signaling by ERBB4 / PIP3 activates AKT signaling / Signaling by SCF-KIT / Regulation of KIT signaling / Signaling by EGFR / GAB1 signalosome / Regulation of gap junction activity / FCGR activation / PECAM1 interactions ...Signaling by ERBB2 / Nuclear signaling by ERBB4 / PIP3 activates AKT signaling / Signaling by SCF-KIT / Regulation of KIT signaling / Signaling by EGFR / GAB1 signalosome / Regulation of gap junction activity / FCGR activation / PECAM1 interactions / CD28 co-stimulation / CTLA4 inhibitory signaling / EPHA-mediated growth cone collapse / Ephrin signaling / G alpha (i) signalling events / GP1b-IX-V activation signalling / Recycling pathway of L1 / Thrombin signalling through proteinase activated receptors (PARs) / VEGFR2 mediated cell proliferation / RAF activation / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / RET signaling / Receptor Mediated Mitophagy / ADP signalling through P2Y purinoceptor 1 / Downregulation of ERBB4 signaling / EPH-ephrin mediated repulsion of cells / Cyclin D associated events in G1 / Regulation of RUNX3 expression and activity / Activated NTRK3 signals through PI3K / Downstream signal transduction / MAP2K and MAPK activation / Integrin signaling / GRB2:SOS provides linkage to MAPK signaling for Integrins / MET activates PTK2 signaling / Extra-nuclear estrogen signaling / EPHB-mediated forward signaling / p130Cas linkage to MAPK signaling for integrins / VEGFA-VEGFR2 Pathway / connexin binding / osteoclast development / progesterone receptor signaling pathway / negative regulation of intrinsic apoptotic signaling pathway / bone resorption / extrinsic component of cytoplasmic side of plasma membrane / negative regulation of extrinsic apoptotic signaling pathway / non-specific protein-tyrosine kinase / non-membrane spanning protein tyrosine kinase activity / epidermal growth factor receptor signaling pathway / cell junction / protein phosphatase binding / protein tyrosine kinase activity / mitochondrial inner membrane / cell differentiation / cytoskeleton / endosome membrane / regulation of cell cycle / cell adhesion / cell cycle / phosphorylation / signaling receptor binding / focal adhesion / innate immune response / heme binding / perinuclear region of cytoplasm / protein-containing complex / ATP binding / membrane / nucleus / plasma membrane / cytosol
Similarity search - Function
SH3 Domains / SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / SH3 type barrels. / Src homology 3 domains / SH2 domain superfamily / SH3-like domain superfamily ...SH3 Domains / SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / SH3 type barrels. / Src homology 3 domains / 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 / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / 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 / molecular replacement / Resolution: 0.95 Å
AuthorsCamara-Artigas, A.
Funding support Spain, 1items
OrganizationGrant numberCountry
Spanish Ministry of Economy and CompetitivenessBIO2016-78020-R Spain
CitationJournal: to be published
Title: High resolution crystal structure of the c-Src-SH3 domain mutant E93V in complex with the high affinity synthetic peptide APP12: monoclinic crystal
Authors: Camara-Artigas, A.
History
DepositionJun 23, 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 1.2Feb 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 1.3Jan 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Proto-oncogene tyrosine-protein kinase Src
B: APP12
C: Proto-oncogene tyrosine-protein kinase Src
D: APP12


Theoretical massNumber of molelcules
Total (without water)16,6354
Polymers16,6354
Non-polymers00
Water2,612145
1
A: Proto-oncogene tyrosine-protein kinase Src
B: APP12


Theoretical massNumber of molelcules
Total (without water)8,3172
Polymers8,3172
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area960 Å2
ΔGint-5 kcal/mol
Surface area3950 Å2
MethodPISA
2
C: Proto-oncogene tyrosine-protein kinase Src
D: APP12


Theoretical massNumber of molelcules
Total (without water)8,3172
Polymers8,3172
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1180 Å2
ΔGint-5 kcal/mol
Surface area4570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.804, 31.801, 61.634
Angle α, β, γ (deg.)90.000, 127.830, 90.000
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 6904.580 Da / Num. of mol.: 2 / Fragment: SH3 DOMAIN, UNP residues 85-141 / Mutation: yes
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.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 145 / 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: 2.15 Å3/Da / Density % sol: 42.9 % / Mosaicity: 0.06 °
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 1.6 M Ammonium sulphate, 0.1 M sodium acetate, 5 mM lithium chloride and 10% Glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97948 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 16, 2016
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: 0.97948 Å / Relative weight: 1
ReflectionResolution: 0.95→19.8 Å / Num. obs: 77638 / % possible obs: 95.7 % / Redundancy: 11.7 % / Biso Wilson estimate: 9.38 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.069 / Rpim(I) all: 0.021 / Rrim(I) all: 0.072 / Net I/σ(I): 17.6 / Num. measured all: 905208 / Scaling rejects: 266
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Rpim(I) allRrim(I) all% possible all
0.95-0.973.30.4250.8190.2680.50657.7
5.2-19.812.40.0650.9980.020.06997.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
Aimless0.5.28data scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4RTW

4rtw


Resolution: 0.95→19.798 Å / SU ML: 0.07 / Cross valid method: THROUGHOUT / σ(F): 0.04 / Phase error: 14.62
RfactorNum. reflection% reflection
Rfree0.1595 7591 5.02 %
Rwork0.1406 --
obs0.1416 77638 95.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 55.28 Å2 / Biso mean: 14.5439 Å2 / Biso min: 5.42 Å2
Refinement stepCycle: final / Resolution: 0.95→19.798 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1044 0 0 145 1189
Biso mean---30.01 -
Num. residues----134
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061136
X-RAY DIFFRACTIONf_angle_d0.9581565
X-RAY DIFFRACTIONf_chiral_restr0.069169
X-RAY DIFFRACTIONf_plane_restr0.008206
X-RAY DIFFRACTIONf_dihedral_angle_d9.812417
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
0.95-0.96080.25761340.24622692282654
0.9608-0.97210.28141710.23513247341865
0.9721-0.9840.25212040.22644197440184
0.984-0.99640.21442650.20624976524198
0.9964-1.00950.20612300.174849875217100
1.0095-1.02330.18572630.158850365299100
1.0233-1.0380.15172500.147349865236100
1.038-1.05350.1362280.138950605288100
1.0535-1.06990.14612780.130950605338100
1.0699-1.08750.15592800.126749375217100
1.0875-1.10620.12992290.129550405269100
1.1062-1.12630.1442740.121150365310100
1.1263-1.1480.13572600.120650035263100
1.148-1.17140.13032940.115950325326100
1.1714-1.19690.12922560.114850475303100
1.1969-1.22470.14042710.123649575228100
1.2247-1.25530.14772520.12350085260100
1.2553-1.28930.12732720.120850375309100
1.2893-1.32720.13452490.123450215270100
1.3272-1.370.15132900.120449745264100
1.37-1.4190.12872840.120549975281100
1.419-1.47580.12722810.122350505331100
1.4758-1.54290.14612540.123450145268100
1.5429-1.62420.14063080.123449395247100
1.6242-1.7260.15152420.125250565298100
1.726-1.85910.13252860.130950105296100
1.8591-2.0460.14891880.1273770395875
2.046-2.34170.13212660.14024469473590
2.3417-2.94870.18622470.158150255272100
2.9487-19.80260.2032850.163449905275100

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