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

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Basic information

Entry
Database: PDB / ID: 4hvv
TitleCrystal structure of the T98E 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 / 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)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 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
Revision 1.3Nov 20, 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: SYNTHETIC PEPTIDE Acetyl-APPLPPRNRP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,0863
Polymers7,9902
Non-polymers961
Water1,31573
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1220 Å2
ΔGint-15 kcal/mol
Surface area4310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)31.588, 31.588, 106.689
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
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: 6847.485 Da / Num. of mol.: 1 / Fragment: SH3 domain / Mutation: T98E, 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 73 / 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: 1.92 Å3/Da / Density % sol: 36.04 %
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: ESRF / Beamline: ID14-4 / Wavelength: 0.97 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 8, 2011
RadiationMonochromator: Si(111) channel-cut crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.1→35.563 Å / Num. all: 26085 / Num. obs: 24885 / % possible obs: 95.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.6 % / Biso Wilson estimate: 10.523 Å2 / Rmerge(I) obs: 0.067 / Net I/σ(I): 19.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique all% possible all
1.1-1.125.50.6672.4485588368.5
5.92-19.19.70.06628.9147415270.1

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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: 1.1→19.097 Å / Occupancy max: 1 / Occupancy min: 0.12 / FOM work R set: 0.9205 / SU ML: 0.08 / Cross valid method: THROUGHOUT / σ(F): 1.15 / σ(I): 0 / Phase error: 14.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1563 2365 5.14 %RANDOM
Rwork0.1436 ---
all0.1442 48366 --
obs0.1442 46049 95.21 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 54.57 Å2 / Biso mean: 19.7255 Å2 / Biso min: 6.18 Å2
Refinement stepCycle: LAST / Resolution: 1.1→19.097 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms536 0 5 73 614
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009571
X-RAY DIFFRACTIONf_angle_d1.214781
X-RAY DIFFRACTIONf_chiral_restr0.07382
X-RAY DIFFRACTIONf_plane_restr0.007101
X-RAY DIFFRACTIONf_dihedral_angle_d12.4211
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 17

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.1001-1.12260.2793810.24961858193968
1.1226-1.1470.24391110.19952098220977
1.147-1.17360.2011100.17452347245786
1.1736-1.2030.17741220.15292520264295
1.203-1.23550.19141670.144326842851100
1.2355-1.27190.17811640.143627202884100
1.2719-1.31290.18571490.129327022851100
1.3129-1.35980.15371490.110626722821100
1.3598-1.41420.10621610.110226692830100
1.4142-1.47860.1271650.113126852850100
1.4786-1.55650.14121700.106426772847100
1.5565-1.6540.13041160.106927462862100
1.654-1.78160.14071670.1126942861100
1.7816-1.96070.1251430.116726922835100
1.9607-2.24410.15641380.124226852823100
2.2441-2.82580.14121260.160827142840100
2.8258-19.10030.181260.17672521264793

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