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- PDB-4rtz: Crystal structure of the c-Src-SH3 domain in complex with the hig... -

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Basic information

Entry
Database: PDB / ID: 4rtz
TitleCrystal structure of the c-Src-SH3 domain in complex with the high affinity peptide VSL12
Components
  • Proto-oncogene tyrosine-protein kinase Src
  • VSL12 peptide
KeywordsPROTEIN BINDING / beta shandwich / SH3 domain
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 / 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 / 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 / progesterone receptor signaling pathway / negative regulation of intrinsic apoptotic signaling pathway / 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 / regulation of cell cycle / endosome membrane / cell adhesion / innate immune response / signaling receptor binding / focal adhesion / 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 / SH3 type barrels. / SH2 domain / Src homology 3 domains / SH2 domain superfamily ...SH3 Domains / : / SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH3 type barrels. / SH2 domain / 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
NICKEL (II) ION / Proto-oncogene tyrosine-protein kinase Src
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.979 Å
AuthorsCamara-Artigas, A. / Bacarizo, J.
CitationJournal: To be Published
Title: Crystal structure of the c-Src-SH3 domain in complex with the high affinity peptide VSL12
Authors: Camara-Artigas, A.
History
DepositionNov 16, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 28, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 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 / pdbx_struct_conn_angle / software / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _software.name / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 650HELIX DETERMINATION METHOD: AUTHOR

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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: VSL12 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,3744
Polymers8,2232
Non-polymers1512
Water1,11762
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1110 Å2
ΔGint-15 kcal/mol
Surface area4400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)32.904, 41.046, 44.066
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 6905.498 Da / Num. of mol.: 1 / Fragment: SH3 domain (UNP residues 85-141)
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 VSL12 peptide


Mass: 1317.622 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Synthetic high affinity peptide
#3: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 62 / 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: 1.81 Å3/Da / Density % sol: 32.02 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1.7 M Ammonium sulphate, 0.1 M Hepes, 5 mM NiCl2 and 10% Glycerol, pH 7.5, vapor diffusion, hanging drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.979491 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 14, 2013
RadiationMonochromator: Channel-cut monochromator and a Kirkpatrick-Baez (KB) focusing system
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979491 Å / Relative weight: 1
ReflectionRedundancy: 3.1 % / Number: 106199 / Rmerge(I) obs: 0.047 / D res high: 0.98 Å / D res low: 41.05 Å / Num. obs: 34334 / % possible obs: 98.1
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)IDRmerge(I) obsRedundancy
0.98110.8362.8
5.2741.0510.0372.7
ReflectionResolution: 0.98→41.05 Å / Num. all: 34999 / Num. obs: 34334 / % possible obs: 98.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Biso Wilson estimate: 9.43 Å2 / Rmerge(I) obs: 0.047 / Net I/σ(I): 12.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique all% possible all
0.98-12.80.8361.44416158689.6
5.27-41.052.70.03729.972926897.7

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Processing

Software
NameVersionClassificationNB
Aimless0.1.30data scaling
PHENIX1.8.4_1496refinement
PDB_EXTRACT3.15data extraction
MOSFLMdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4JZ4

4jz4


Resolution: 0.979→30.035 Å / SU ML: 0.09 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0.01 / Phase error: 15.71 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1584 3256 5 %random
Rwork0.1427 ---
obs0.1435 65154 98.11 %-
all-66409 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 49.48 Å2 / Biso mean: 14.6664 Å2 / Biso min: 6.83 Å2
Refinement stepCycle: LAST / Resolution: 0.979→30.035 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms549 0 7 62 618
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009591
X-RAY DIFFRACTIONf_angle_d1.381811
X-RAY DIFFRACTIONf_chiral_restr0.08387
X-RAY DIFFRACTIONf_plane_restr0.007106
X-RAY DIFFRACTIONf_dihedral_angle_d11.098216
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 (%)
0.9791-0.99370.28981120.3122452256488
0.9937-1.00920.26781230.30712652277597
1.0092-1.02580.30141330.28472686281996
1.0258-1.04350.23771370.24522635277298
1.0435-1.06250.2251340.21512705283998
1.0625-1.08290.20051370.18122668280598
1.0829-1.1050.16091470.17342747289499
1.105-1.1290.15731440.15662681282599
1.129-1.15530.16211270.14452683281098
1.1553-1.18420.14441570.13862700285799
1.1842-1.21620.15391710.13292681285299
1.2162-1.2520.15191480.12872746289499
1.252-1.29240.14551420.13012711285399
1.2924-1.33860.15141520.12582699285199
1.3386-1.39220.13821200.121127622882100
1.3922-1.45560.13141240.118527382862100
1.4556-1.53230.1131610.117227272888100
1.5323-1.62830.13961760.1252707288399
1.6283-1.7540.20071290.12652711284098
1.754-1.93050.16071190.12872736285599
1.9305-2.20970.1361610.1292701286299
2.2097-2.78370.17941680.14652670283898
2.7837-30.0490.14691340.14132700283498

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