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- PDB-4hvu: Crystal structure of the T98D c-Src-SH3 domain mutant in complex ... -

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Basic information

Entry
Database: PDB / ID: 4hvu
TitleCrystal structure of the T98D c-Src-SH3 domain mutant in complex with the high affinity peptide APP12
Components
  • Proto-oncogene tyrosine-protein kinase Src
  • SYNTHETIC PEPTIDE Acetyl-APPLPPRNRP
KeywordsSignaling Protein/Peptide / beta shandwich / SH3 like barrel / Kinase / Proline Rich Motifs / Signaling Protein-Peptide complex
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 / immune system process / 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-cell junction / cell junction / protein tyrosine kinase activity / protein phosphatase binding / cell differentiation / cytoskeleton / regulation of cell cycle / cell adhesion / mitochondrial inner membrane / 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 / SH3 type barrels. / Src homology 3 domains / SH2 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 / 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
ACETYL GROUP / Proto-oncogene tyrosine-protein kinase Src
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.98 Å
AuthorsCamara-Artigas, A.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2013
Title: Atomic resolution structures of the c-Src SH3 domain in complex with two high-affinity peptides from classes I and II.
Authors: Bacarizo, J. / Camara-Artigas, A.
History
DepositionNov 7, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 1, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2013Group: Database references
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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: SYNTHETIC PEPTIDE Acetyl-APPLPPRNRP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,2755
Polymers8,0912
Non-polymers1843
Water1,60389
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1630 Å2
ΔGint-16 kcal/mol
Surface area4330 Å2
MethodPISA
2
A: Proto-oncogene tyrosine-protein kinase Src
B: SYNTHETIC PEPTIDE Acetyl-APPLPPRNRP
hetero molecules

A: Proto-oncogene tyrosine-protein kinase Src
B: SYNTHETIC PEPTIDE Acetyl-APPLPPRNRP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,55010
Polymers16,1824
Non-polymers3686
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_645y+1,x-1,-z1
Buried area4720 Å2
ΔGint-37 kcal/mol
Surface area7210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)31.503, 31.503, 106.710
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-93-

GLU

21A-375-

HOH

Detailsbiological unit is the same as asym.

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Components

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


Mass: 6948.547 Da / Num. of mol.: 1 / Fragment: SH3 domain / Mutation: T98D, Q128R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: SRC / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P00523, non-specific protein-tyrosine kinase
#2: Protein/peptide SYNTHETIC PEPTIDE Acetyl-APPLPPRNRP


Mass: 1142.353 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: High affinity peptide designed from phage display experiments
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-ACE / ACETYL GROUP


Mass: 44.053 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H4O
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 89 / 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: 1.89 Å3/Da / Density % sol: 34.89 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 1.7 M Ammonium sulphate, 10% PEG 300, 10% glycerol and 0.1 M sodium acetate, pH 5, vapor diffusion, hanging drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97951 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 13, 2012
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: 0.97951 Å / Relative weight: 1
ReflectionResolution: 0.98→35.57 Å / Num. all: 36286 / Num. obs: 35524 / % possible obs: 97.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.8 % / Biso Wilson estimate: 10.023 Å2 / Rmerge(I) obs: 0.037 / Net I/σ(I): 29.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique all% possible all
0.98-11.80.1693.92555141882.8
5.37-19.073.10.04836.873523685.8

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Processing

Software
NameVersionClassificationNB
Aimless0.1.27data scaling
PHENIX1.8_1069refinement
PDB_EXTRACT3.11data extraction
ADSCQuantumdata collection
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3FJ5

3fj5


Resolution: 0.98→19.074 Å / Occupancy max: 1 / Occupancy min: 0.1 / FOM work R set: 0.9381 / SU ML: 0.07 / Cross valid method: THROUGHOUT / σ(F): 1.44 / σ(I): 0 / Phase error: 11.54 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.16 3221 5 %RANDOM
Rwork0.1449 ---
all0.1456 68001 --
obs0.1456 64397 94.7 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 48.09 Å2 / Biso mean: 18.5467 Å2 / Biso min: 6.32 Å2
Refinement stepCycle: LAST / Resolution: 0.98→19.074 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms544 0 11 89 644
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011577
X-RAY DIFFRACTIONf_angle_d1.551783
X-RAY DIFFRACTIONf_chiral_restr0.08682
X-RAY DIFFRACTIONf_plane_restr0.011102
X-RAY DIFFRACTIONf_dihedral_angle_d11.022210
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 23

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
0.98-0.99470.186830.18391600168358
0.9947-1.01020.1751900.18532073216372
1.0102-1.02680.16281300.16622300243083
1.0268-1.04450.1431420.1452527266990
1.0445-1.06350.12571490.13322676282596
1.0635-1.08390.13361530.11292788294198
1.0839-1.1060.12641440.11082731287599
1.106-1.13010.11051250.10362853297898
1.1301-1.15640.13581360.09722750288699
1.1564-1.18530.11591710.10542766293799
1.1853-1.21730.14511550.10342767292299
1.2173-1.25320.12761590.10842778293799
1.2532-1.29360.1391240.10952753287799
1.2936-1.33980.15011610.10292790295199
1.3398-1.39340.11771570.100327962953100
1.3934-1.45680.14411740.10422774294899
1.4568-1.53360.12771450.103427752920100
1.5336-1.62970.13291220.107828392961100
1.6297-1.75540.15961550.11528463001100
1.7554-1.93190.13711180.123428152933100
1.9319-2.21110.11811550.1327732928100
2.2111-2.78440.17481410.168428202961100
2.7844-19.07770.23681320.22242586271892

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