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- PDB-3of0: crystal structure of the L317I mutant of the chicken c-Src tyrosi... -

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Basic information

Entry
Database: PDB / ID: 3of0
Titlecrystal structure of the L317I mutant of the chicken c-Src tyrosine kinase domain
ComponentsProto-oncogene tyrosine-protein kinase Src
KeywordsTRANSFERASE / c-Src L317I mutant / tyrosine kinase
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 domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / Src homology 3 domains / SH2 domain superfamily / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain ...SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / 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 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha 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: 2.7 Å
AuthorsBoubeva, R. / Pernot, L. / Perozzo, R. / Scapozza, L.
Citation
Journal: To be Published
Title: a single amino-acid dictates the dynamics of the switch between active and inactive C-Src conformation
Authors: Boubeva, R. / Pernot, L. / Cristiani, A. / Moretti, L. / Berteotti, A. / Perozzo, R. / Gervasio, F. / Scapozza, L.
#1: Journal: Structure / Year: 2007
Title: c-Src binds to the cancer drug imatinib with an inactive Abl/c-Kit conformation and a distributed thermodynamic penalty.
Authors: Seeliger, M.A. / Nagar, B. / Frank, F. / Cao, X. / Henderson, M.N. / Kuriyan, J.
History
DepositionAug 13, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 17, 2011Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2023Group: 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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: Proto-oncogene tyrosine-protein kinase Src


Theoretical massNumber of molelcules
Total (without water)65,4532
Polymers65,4532
Non-polymers00
Water4,342241
1
A: Proto-oncogene tyrosine-protein kinase Src


Theoretical massNumber of molelcules
Total (without water)32,7271
Polymers32,7271
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Proto-oncogene tyrosine-protein kinase Src


Theoretical massNumber of molelcules
Total (without water)32,7271
Polymers32,7271
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.072, 63.496, 74.126
Angle α, β, γ (deg.)78.66, 89.41, 90.00
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22
13
23
14
24
15
25
16
26
17
27

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN A AND (RESSEQ 319:326 )
211CHAIN B AND (RESSEQ 319:326 )
112CHAIN A AND (RESSEQ 338:339 )
212CHAIN B AND (RESSEQ 338:339 )
113CHAIN A AND (RESSEQ 360:378 )
213CHAIN B AND (RESSEQ 360:378 )
114CHAIN A AND (RESSEQ 441:465 )
214CHAIN B AND (RESSEQ 441:465 )
115CHAIN A AND (RESSEQ 481:492 )
215CHAIN B AND (RESSEQ 481:492 )
116CHAIN A AND (RESSEQ 496:498 )
216CHAIN B AND (RESSEQ 496:498 )
117CHAIN A AND (RESSEQ 503:523 )
217CHAIN B AND (RESSEQ 503:523 )

NCS ensembles :
ID
1
2
3
4
5
6
7

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Components

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


Mass: 32726.645 Da / Num. of mol.: 2 / Fragment: kinase domain / Mutation: L317I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: SRC / Plasmid: pET28a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P00523, non-specific protein-tyrosine kinase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 241 / 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: 2.97 Å3/Da / Density % sol: 58.53 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 100 mM MES, 200 mM sodium acetate, 4% glycerol, 12% PEG 4000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 31, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→32.8 Å / Num. obs: 20128 / % possible obs: 97.3 % / Observed criterion σ(I): 2 / Redundancy: 3.9 % / Biso Wilson estimate: 44.1 Å2 / Rmerge(I) obs: 0.159 / Rsym value: 0.116 / Net I/σ(I): 9.4
Reflection shellResolution: 2.7→2.85 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.537 / Mean I/σ(I) obs: 2.97 / Num. unique all: 2943 / Rsym value: 0.388 / % possible all: 97.3

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Processing

Software
NameVersionClassification
PHASERphasing
PHENIX(phenix.refine)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3OEZ

3oez


Resolution: 2.7→32.778 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 2.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2615 977 4.86 %RANDOM
Rwork0.2334 ---
obs0.2348 20120 97.35 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 34.435 Å2 / ksol: 0.34 e/Å3
Displacement parametersBiso mean: 38.95 Å2
Baniso -1Baniso -2Baniso -3
1--9.3737 Å2-1.7838 Å2-0.1916 Å2
2--0.9167 Å21.9652 Å2
3---4.4157 Å2
Refinement stepCycle: LAST / Resolution: 2.7→32.778 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4056 0 0 241 4297
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034152
X-RAY DIFFRACTIONf_angle_d0.6835625
X-RAY DIFFRACTIONf_dihedral_angle_d17.8651521
X-RAY DIFFRACTIONf_chiral_restr0.046608
X-RAY DIFFRACTIONf_plane_restr0.003721
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A72X-RAY DIFFRACTIONPOSITIONAL
12B72X-RAY DIFFRACTIONPOSITIONAL0.009
21A16X-RAY DIFFRACTIONPOSITIONAL
22B16X-RAY DIFFRACTIONPOSITIONAL0.01
31A138X-RAY DIFFRACTIONPOSITIONAL
32B138X-RAY DIFFRACTIONPOSITIONAL0.005
41A196X-RAY DIFFRACTIONPOSITIONAL
42B196X-RAY DIFFRACTIONPOSITIONAL0.005
51A90X-RAY DIFFRACTIONPOSITIONAL
52B90X-RAY DIFFRACTIONPOSITIONAL0.008
61A21X-RAY DIFFRACTIONPOSITIONAL
62B21X-RAY DIFFRACTIONPOSITIONAL0.008
71A183X-RAY DIFFRACTIONPOSITIONAL
72B183X-RAY DIFFRACTIONPOSITIONAL0.012
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.84230.2921380.2512739X-RAY DIFFRACTION97
2.8423-3.02020.27351310.24612752X-RAY DIFFRACTION97
3.0202-3.25320.24151620.2352692X-RAY DIFFRACTION97
3.2532-3.58030.25851420.20632716X-RAY DIFFRACTION97
3.5803-4.09750.24641340.20532739X-RAY DIFFRACTION98
4.0975-5.15920.22851390.20242747X-RAY DIFFRACTION98
5.1592-32.78080.26521310.24862758X-RAY DIFFRACTION98
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.19890.2130.20440.817-0.18660.51530.22140.00550.01290.27120.0486-0.1520.2234-0.2017-0.05830.4016-0.07920.00160.2720.07-0.0026-12.021-37.205318.2037
20.88830.06350.6420.3709-0.0641-0.45240.0895-0.0949-0.01350.10360.267-0.15650.41070.8008-0.27740.7064-0.02340.10060.6343-0.0520.1033-6.9166-44.90359.0703
31.75280.0251-0.09810.46470.122.6519-0.1644-0.6361-0.01570.0007-0.32660.0136-0.52081.25330.42260.5653-0.1726-0.20031.0860.25020.28141.3143-32.286114.2482
41.50380.78150.79930.12910.46060.52990.00990.4851-0.31860.35590.1636-0.4591-0.15730.2963-0.08990.20320.010.05760.19870.06890.35443.8878-34.9985-2.4535
50.7263-0.08120.06590.88930.07681.1630.14460.1850.0697-0.0384-0.1752-0.07990.07470.25520.0188-0.0277-0.094-0.0094-0.00630.00720.0745-3.2239-28.2965-8.4111
60.9808-0.43760.12121.271-0.13410.80430.58220.7522-0.0621-1.3774-0.1665-0.17791.4060.4383-0.22290.71750.1877-0.01070.42790.06090.1598-4.3996-67.9269-45.0084
70.0324-1.07290.10351.28810.0421.20980.3627-0.07330.0087-0.3730.43510.27140.0288-0.3547-0.47271.0182-0.0157-0.02460.5120.14050.2923-9.0931-76.1984-34.8338
81.0795-0.5880.01560.6312-0.54141.7482-0.37440.1393-0.25710.169-0.30080.0093-0.1058-0.39330.32430.23790.05060.15160.8020.00970.284-17.9479-60.8311-41.0665
92.0351-1.20850.95093.38670.90441.2093-0.2175-0.3356-0.248-0.4935-0.02530.5765-0.1209-0.50430.13180.0831-0.09180.00020.202-0.1120.1905-18.9018-66.6229-24.4836
100.42660.48720.15730.972-0.38021.39640.0014-0.12380.0585-0.0628-0.06-0.01680.0365-0.20020.0342-0.01130.03780.00140.062-0.02870.0933-11.8573-59.752-17.6201
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID 257:272 OR RESI 284:298)
2X-RAY DIFFRACTION2CHAIN A AND RESID 273:283
3X-RAY DIFFRACTION3CHAIN A AND RESID 299:318
4X-RAY DIFFRACTION4CHAIN A AND RESID 403:427
5X-RAY DIFFRACTION5CHAIN A AND (RESID 319:402 OR RESI 428:533)
6X-RAY DIFFRACTION6CHAIN B AND (RESID 257:272 OR RESI 284:296)
7X-RAY DIFFRACTION7CHAIN B AND RESID 273:283
8X-RAY DIFFRACTION8CHAIN B AND RESID 302:318
9X-RAY DIFFRACTION9CHAIN B AND RESID 403:427
10X-RAY DIFFRACTION10CHAIN B AND (RESID 319:330 OR RESI 335:402)

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