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- PDB-4hvw: Crystal structure of the T98E c-Src-SH3 domain mutant in complex ... -

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Basic information

Entry
Database: PDB / ID: 4hvw
TitleCrystal structure of the T98E c-Src-SH3 domain mutant in complex with the high affinity peptide VSL12
Components
  • Proto-oncogene tyrosine-protein kinase Src
  • SYNTHETIC PEPTIDE Acetyl-VSLARRPLPPLP
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 / 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 / Src homology 3 domains / SH3 type barrels. / 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 / 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 / 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
ACETYL GROUP / Proto-oncogene tyrosine-protein kinase Src
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / 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-VSLARRPLPPLP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,4464
Polymers8,3062
Non-polymers1402
Water1,45981
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1490 Å2
ΔGint-18 kcal/mol
Surface area5040 Å2
MethodPISA
2
A: Proto-oncogene tyrosine-protein kinase Src
B: SYNTHETIC PEPTIDE Acetyl-VSLARRPLPPLP
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)16,8938
Polymers16,6124
Non-polymers2804
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_465y-1,x+1,-z1
Buried area5030 Å2
ΔGint-55 kcal/mol
Surface area8030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.442, 37.442, 85.624
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-359-

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: 6962.573 Da / Num. of mol.: 1 / Fragment: SH3 domain / Mutation: T98E, T125S, 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-VSLARRPLPPLP


Mass: 1343.660 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: High affinity peptide designed from phage display experiments
#3: Chemical ChemComp-ACE / ACETYL GROUP / Acetyl group


Mass: 44.053 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


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


Mass: 18.015 Da / Num. of mol.: 81 / 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: 2.09 Å3/Da / Density % sol: 41.13 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 1.7 M Ammonium sulphate, 5% PEG 300, 10% glycerol and 0.1 M sodium acetate, 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→32.426 Å / Num. obs: 72675 / % possible obs: 98.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Biso Wilson estimate: 8.337 Å2 / Rmerge(I) obs: 0.051 / Net I/σ(I): 19.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
0.98-11.60.1623.4181.4
5.19-18.7240.05829.7196.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
Aimless0.1.27data scaling
PHASERphasing
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.11data extraction
ADSCQuantumdata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3FJ5

3fj5


Resolution: 0.98→18.721 Å / Occupancy max: 1 / Occupancy min: 0.22 / SU ML: 0.06 / σ(F): 1.33 / Phase error: 10.53 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1414 3647 5.02 %
Rwork0.1337 --
obs0.134 72675 94.23 %
all-77128 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 14.4743 Å2
Refinement stepCycle: LAST / Resolution: 0.98→18.721 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms588 0 8 81 677
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009675
X-RAY DIFFRACTIONf_angle_d1.49925
X-RAY DIFFRACTIONf_dihedral_angle_d10.475248
X-RAY DIFFRACTIONf_chiral_restr0.076100
X-RAY DIFFRACTIONf_plane_restr0.009123
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
0.98-0.99290.1644720.16931611X-RAY DIFFRACTION57
0.9929-1.00650.1772950.17171873X-RAY DIFFRACTION66
1.0065-1.02090.17081320.1572121X-RAY DIFFRACTION77
1.0209-1.03620.16761440.1472414X-RAY DIFFRACTION86
1.0362-1.05230.14411450.12862653X-RAY DIFFRACTION94
1.0523-1.06960.13061590.11622715X-RAY DIFFRACTION97
1.0696-1.0880.11321130.10782798X-RAY DIFFRACTION98
1.088-1.10780.12361380.09872729X-RAY DIFFRACTION98
1.1078-1.12910.10421450.09432794X-RAY DIFFRACTION98
1.1291-1.15220.11111440.09142785X-RAY DIFFRACTION99
1.1522-1.17720.10021100.09232787X-RAY DIFFRACTION98
1.1772-1.20460.11461450.09722836X-RAY DIFFRACTION99
1.2046-1.23470.10531590.09392692X-RAY DIFFRACTION98
1.2347-1.26810.11681500.0962801X-RAY DIFFRACTION99
1.2681-1.30540.08911330.09682796X-RAY DIFFRACTION99
1.3054-1.34750.11341490.0982767X-RAY DIFFRACTION98
1.3475-1.39570.11081690.09812787X-RAY DIFFRACTION100
1.3957-1.45150.12261640.09382796X-RAY DIFFRACTION99
1.4515-1.51760.12551660.09752745X-RAY DIFFRACTION99
1.5176-1.59750.11231740.10062775X-RAY DIFFRACTION99
1.5975-1.69760.10711100.11452798X-RAY DIFFRACTION98
1.6976-1.82850.12541600.12722749X-RAY DIFFRACTION99
1.8285-2.01240.12221400.13182812X-RAY DIFFRACTION100
2.0124-2.30310.14331710.13472792X-RAY DIFFRACTION99
2.3031-2.89990.21231300.16432811X-RAY DIFFRACTION99
2.8999-18.72440.18441300.1862791X-RAY DIFFRACTION99

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