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- PDB-5ec7: Crystal structure of a chimeric c-Src-SH3 domain with the sequenc... -

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Basic information

Entry
Database: PDB / ID: 5ec7
TitleCrystal structure of a chimeric c-Src-SH3 domain with the sequence of the RT-loop from the Abl-SH3 domain at pH 5.0
ComponentsProto-oncogene tyrosine-protein kinase Src
KeywordsTRANSFERASE / beta shandwich
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 / 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 / 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
DI(HYDROXYETHYL)ETHER / Proto-oncogene tyrosine-protein kinase Src
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.65 Å
AuthorsCamara-Artigas, A.
Funding support Spain, 2items
OrganizationGrant numberCountry
Agencia de Innovacion y Desarrollo de AndaluciaP09-CVI-5063 Spain
Spanish Ministry of Economy and CompetitivenessBIO2012-39922-C02-02 Spain
CitationJournal: to be published
Title: Crystal structure of a chimeric c-Src-SH3 domain with the sequence of the RT-loop from the Abl-SH3 domain at pH 5.0
Authors: Camara-Artigas, A.
History
DepositionOct 20, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Nov 9, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2017Group: Author supporting evidence / Data collection / Category: diffrn_radiation_wavelength / pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Jan 10, 2024Group: 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 / software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.name

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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
C: Proto-oncogene tyrosine-protein kinase Src
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,5567
Polymers19,1313
Non-polymers4244
Water1,838102
1
A: Proto-oncogene tyrosine-protein kinase Src
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,5893
Polymers6,3771
Non-polymers2122
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Proto-oncogene tyrosine-protein kinase Src
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,4832
Polymers6,3771
Non-polymers1061
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Proto-oncogene tyrosine-protein kinase Src
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,4832
Polymers6,3771
Non-polymers1061
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)83.472, 42.348, 52.579
Angle α, β, γ (deg.)90.000, 90.470, 90.000
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 6377.048 Da / Num. of mol.: 3 / Fragment: SH3 DOMAIN / Mutation: E93V; S94A; R95S; Q128R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: SRC / Plasmid: pET15b / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P00523, non-specific protein-tyrosine kinase
#2: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 102 / 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: 2.43 Å3/Da / Density % sol: 49.36 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 2.5 M ammonium sulphate, 5% PEG 300, 2 % Glycerol, 0.1 M sodium acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 20, 2015
RadiationMonochromator: Channel-cut double crystal monochromator (CINEL), cryocooled, 6mm gap
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.65→19.64 Å / Num. obs: 21249 / % possible obs: 95.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.8 % / Biso Wilson estimate: 16.33 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.054 / Rpim(I) all: 0.039 / Net I/σ(I): 11.7 / Num. measured all: 59267
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
1.65-1.682.90.4392.3311610830.7460.3196.2
8.89-19.642.60.02727.43671390.9980.01887.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
autoPROCdata reduction
Aimless0.5.12data scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4JZ4

4jz4


Resolution: 1.65→19.64 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 0.17 / Phase error: 22.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2431 2060 4.97 %
Rwork0.1908 39420 -
obs0.1933 41480 95.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 73.51 Å2 / Biso mean: 26.2862 Å2 / Biso min: 6.41 Å2
Refinement stepCycle: final / Resolution: 1.65→19.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1265 0 68 102 1435
Biso mean--43.76 33.11 -
Num. residues----169
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081323
X-RAY DIFFRACTIONf_angle_d0.9321803
X-RAY DIFFRACTIONf_chiral_restr0.059201
X-RAY DIFFRACTIONf_plane_restr0.006226
X-RAY DIFFRACTIONf_dihedral_angle_d12.132731
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.65-1.68840.30791010.26732655X-RAY DIFFRACTION95
1.6884-1.73060.28841700.25482555X-RAY DIFFRACTION95
1.7306-1.77730.26621600.23052557X-RAY DIFFRACTION94
1.7773-1.82960.27071210.22032611X-RAY DIFFRACTION95
1.8296-1.88860.2861500.20632616X-RAY DIFFRACTION95
1.8886-1.9560.22421460.19022655X-RAY DIFFRACTION97
1.956-2.03430.22981540.18832624X-RAY DIFFRACTION97
2.0343-2.12680.20921490.18312678X-RAY DIFFRACTION97
2.1268-2.23870.22991520.17492638X-RAY DIFFRACTION97
2.2387-2.37880.25021570.17082622X-RAY DIFFRACTION97
2.3788-2.56210.23591220.18872678X-RAY DIFFRACTION98
2.5621-2.81930.23641190.19062755X-RAY DIFFRACTION98
2.8193-3.22560.29871060.19662631X-RAY DIFFRACTION96
3.2256-4.05810.24141510.18032566X-RAY DIFFRACTION94
4.0581-19.640.21041020.18292579X-RAY DIFFRACTION93
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)
10.003-0.0047-0.00360.01060.00940.0017-0.0745-0.0415-0.03150.0916-0.01010.0570.10130.054500.14660.0040.02190.0819-0.02160.125620.3144-0.52466.687
20.00980.00020.00210.00380.00320.0072-0.03790.00670.00740.0566-0.02890.03310.01110.0072-0.00820.1179-0.01730.01880.0682-0.0270.101318.46282.32348.241
30.00110.0018-0.00070.0098-0.00580.00320.00560.01160.007-0.0463-0.0615-0.00820.02330.0005-0.00620.14950.01080.01990.1093-0.03930.127818.05022.7072-2.9453
40.01480.00990.02210.00920.01970.032-0.06130.0716-0.01180.05390.0096-0.0344-0.0090.0228-0.01840.102-0.00010.01270.04490.00580.095422.71621.7521-0.3833
50.0477-0.01510.03470.0136-0.02510.0645-0.04050.03690.016-0.0109-0.03090.0557-0.04370.04-0.02190.1498-0.0080.0190.0186-0.02510.092720.812-2.59492.6131
60.00310.00040.00710.00310.00240.0345-0.0041-0.0087-0.00650.0229-0.00580.0183-0.0017-0.001600.2086-0.02760.14090.28450.00230.31851.417513.442919.0664
70.0075-0.0062-0.01260.00420.00770.00810.0251-0.0175-0.0448-0.093-0.08750.0751-0.0787-0.0324-00.0999-0.0010.02310.114-0.00590.18016.777619.24618.9437
80.02070.0070.00960.00270.00320.0033-0.052-0.034-0.01320.0257-0.0009-0.0082-0.0063-0.025-0.02740.26180.12010.12570.27610.03850.20957.552216.502621.2475
90.0022-0.0050.00580.0125-0.02040.0395-0.0142-0.0025-0.00920.0005-0.04730.0248-0.0263-0.005-00.1750.06370.02580.22060.00350.16084.26327.853821.6339
100.00180.0020.00040.0057-0.00340.0122-0.054-0.0076-0.02340.0004-0.01710.0242-0.0192-0.0342-0.03580.13290.0730.09930.18330.04270.129810.107916.914816.3098
110.0353-0.0017-0.01550.0290.01750.0169-0.0397-0.00450.00450.0209-0.03810.06180.00370.0015-0.0250.06120.03620.05220.2104-0.04380.19253.088420.185915.6442
120.00070.0016-0.00510.0412-0.01760.0213-0.0897-0.07870.0846-0.01060.01320.0084-0.1359-0.133-0.03980.2750.1592-0.14560.3896-0.20320.006629.93412.497625.6277
130.0148-0.0010.01390.09150.02450.0435-0.0386-0.04080.050.06340.026-0.0476-0.02330.01280.02110.23180.0301-0.21180.0583-0.10590.198633.055514.95617.3626
140.03560.039-0.02740.0509-0.04260.0283-0.055-0.06260.01340.0019-0.0568-0.0225-0.0339-0.0413-0.0310.12570.0584-0.05360.1619-0.06950.135326.190311.457915.4128
150.00660.0294-0.04510.0969-0.1550.2372-0.1246-0.0330.06510.0458-0.1305-0.0305-0.1645-0.1267-0.14660.15730.0829-0.08320.2598-0.10910.169231.330513.755121.2199
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 84 through 98 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 99 through 106 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 107 through 112 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 113 through 128 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 129 through 140 )A0
6X-RAY DIFFRACTION6chain 'B' and (resid 84 through 88 )B0
7X-RAY DIFFRACTION7chain 'B' and (resid 89 through 106 )B0
8X-RAY DIFFRACTION8chain 'B' and (resid 107 through 112 )B0
9X-RAY DIFFRACTION9chain 'B' and (resid 113 through 117 )B0
10X-RAY DIFFRACTION10chain 'B' and (resid 118 through 128 )B0
11X-RAY DIFFRACTION11chain 'B' and (resid 129 through 140 )B0
12X-RAY DIFFRACTION12chain 'C' and (resid 85 through 104 )C0
13X-RAY DIFFRACTION13chain 'C' and (resid 105 through 112 )C0
14X-RAY DIFFRACTION14chain 'C' and (resid 113 through 123 )C0
15X-RAY DIFFRACTION15chain 'C' and (resid 124 through 139 )C0

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