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- PDB-4hxj: Crystal structure of SH3:RGT complex -

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Basic information

Entry
Database: PDB / ID: 4hxj
TitleCrystal structure of SH3:RGT complex
Components
  • C-terminal 3-mer peptide from Integrin beta-3
  • Proto-oncogene tyrosine-protein kinase Src
KeywordsBLOOD CLOTTING / SIGNALING PROTEIN / integrin beta-3 / c-Src kinase / SH3 domain / RGT / thrombosis / cell signaling
Function / homology
Function and homology information


regulation of toll-like receptor 3 signaling pathway / positive regulation of non-membrane spanning protein tyrosine kinase activity / primary ovarian follicle growth / regulation of caveolin-mediated endocytosis / positive regulation of ovarian follicle development / cellular response to prolactin / positive regulation of platelet-derived growth factor receptor-beta signaling pathway / positive regulation of male germ cell proliferation / dendritic filopodium / regulation of cell projection assembly ...regulation of toll-like receptor 3 signaling pathway / positive regulation of non-membrane spanning protein tyrosine kinase activity / primary ovarian follicle growth / regulation of caveolin-mediated endocytosis / positive regulation of ovarian follicle development / cellular response to prolactin / positive regulation of platelet-derived growth factor receptor-beta signaling pathway / positive regulation of male germ cell proliferation / dendritic filopodium / regulation of cell projection assembly / regulation of cell-cell adhesion / positive regulation of dephosphorylation / response to mineralocorticoid / Regulation of commissural axon pathfinding by SLIT and ROBO / tube development / ERBB2 signaling pathway / regulation of serotonin uptake / positive regulation of adenylate cyclase-inhibiting opioid receptor signaling pathway / alpha9-beta1 integrin-ADAM8 complex / regulation of trophoblast cell migration / regulation of epithelial cell migration / regulation of postsynaptic neurotransmitter receptor diffusion trapping / entry of bacterium into host cell / positive regulation of protein transport / Regulation of gap junction activity / alphav-beta3 integrin-vitronectin complex / regulation of vascular permeability / BMP receptor binding / positive regulation of lamellipodium morphogenesis / maintenance of postsynaptic specialization structure / cellular response to progesterone stimulus / positive regulation of integrin activation / regulation of extracellular matrix organization / Activated NTRK2 signals through FYN / platelet alpha granule membrane / negative regulation of focal adhesion assembly / positive regulation of protein processing / positive regulation of glomerular mesangial cell proliferation / skeletal muscle cell proliferation / integrin alphav-beta3 complex / negative regulation of lipoprotein metabolic process / alphav-beta3 integrin-PKCalpha complex / fibrinogen binding / glycinergic synapse / negative regulation of telomerase activity / intestinal epithelial cell development / Netrin mediated repulsion signals / alphav-beta3 integrin-HMGB1 complex / regulation of intracellular estrogen receptor signaling pathway / blood coagulation, fibrin clot formation / negative regulation of lipid transport / CD28 co-stimulation / vascular endothelial growth factor receptor 2 binding / positive regulation of glucose metabolic process / negative regulation of low-density lipoprotein receptor activity / regulation of release of sequestered calcium ion into cytosol / angiogenesis involved in wound healing / Elastic fibre formation / transcytosis / cell-substrate junction assembly / Activated NTRK3 signals through PI3K / mesodermal cell differentiation / connexin binding / cellular response to fluid shear stress / alphav-beta3 integrin-IGF-1-IGF1R complex / focal adhesion assembly / response to acidic pH / platelet-derived growth factor receptor binding / signal complex assembly / podosome / positive regulation of small GTPase mediated signal transduction / filopodium membrane / positive regulation of fibroblast migration / positive regulation of Ras protein signal transduction / extracellular matrix binding / regulation of postsynaptic neurotransmitter receptor internalization / positive regulation of vascular endothelial growth factor receptor signaling pathway / apolipoprotein A-I-mediated signaling pathway / Regulation of RUNX1 Expression and Activity / regulation of bone resorption / positive regulation of podosome assembly / branching involved in mammary gland duct morphogenesis / apoptotic cell clearance / wound healing, spreading of epidermal cells / DCC mediated attractive signaling / positive regulation of cell adhesion mediated by integrin / heterotypic cell-cell adhesion / integrin complex / adherens junction organization / EPH-Ephrin signaling / myoblast proliferation / Ephrin signaling / osteoclast development / negative regulation of mitochondrial depolarization / odontogenesis / Molecules associated with elastic fibres / cellular response to peptide hormone stimulus / Signal regulatory protein family interactions / positive regulation of cell-matrix adhesion / cellular response to insulin-like growth factor stimulus
Similarity search - Function
Integrin beta, epidermal growth factor-like domain 1 / Integrin beta epidermal growth factor like domain 1 / Integrin beta subunit, cytoplasmic domain / Integrin beta cytoplasmic domain / Integrin_b_cyt / Integrin beta tail domain / Integrin beta subunit, tail / Integrin beta tail domain superfamily / Integrin_B_tail / Integrin beta subunit, VWA domain ...Integrin beta, epidermal growth factor-like domain 1 / Integrin beta epidermal growth factor like domain 1 / Integrin beta subunit, cytoplasmic domain / Integrin beta cytoplasmic domain / Integrin_b_cyt / Integrin beta tail domain / Integrin beta subunit, tail / Integrin beta tail domain superfamily / Integrin_B_tail / Integrin beta subunit, VWA domain / Integrin beta subunit / Integrin beta N-terminal / Integrin beta chain VWA domain / Integrin plexin domain / Integrins beta chain cysteine-rich domain signature. / Integrin beta subunits (N-terminal portion of extracellular region) / EGF-like domain, extracellular / EGF-like domain / Integrin domain superfamily / PSI domain / domain found in Plexins, Semaphorins and Integrins / SH3 Domains / von Willebrand factor A-like domain superfamily / EGF-like domain signature 2. / EGF-like domain signature 1. / 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 / 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
Integrin beta-3 / Proto-oncogene tyrosine-protein kinase Src
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsXiao, R. / Meng, G.
CitationJournal: Blood / Year: 2013
Title: Structural framework of c-Src activation by integrin beta 3
Authors: Xiao, R. / Xi, X.D. / Chen, Z. / Chen, S.J. / Meng, G.
History
DepositionNov 11, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 28, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 5, 2012Group: Database references
Revision 1.2Mar 19, 2014Group: Database references
Revision 1.3Nov 8, 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

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Assembly

Deposited unit
A: Proto-oncogene tyrosine-protein kinase Src
B: Proto-oncogene tyrosine-protein kinase Src
C: C-terminal 3-mer peptide from Integrin beta-3


Theoretical massNumber of molelcules
Total (without water)13,7803
Polymers13,7803
Non-polymers00
Water1,71195
1
A: Proto-oncogene tyrosine-protein kinase Src
C: C-terminal 3-mer peptide from Integrin beta-3


Theoretical massNumber of molelcules
Total (without water)7,0572
Polymers7,0572
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area390 Å2
ΔGint-0 kcal/mol
Surface area3900 Å2
MethodPISA
2
B: Proto-oncogene tyrosine-protein kinase Src


Theoretical massNumber of molelcules
Total (without water)6,7231
Polymers6,7231
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)27.980, 40.830, 43.340
Angle α, β, γ (deg.)90.00, 105.97, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 6723.233 Da / Num. of mol.: 2 / Fragment: human c-Src SH3 domain, UNP residues 87-144
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SRC, SRC1 / Plasmid: pET32a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P12931, non-specific protein-tyrosine kinase
#2: Protein/peptide C-terminal 3-mer peptide from Integrin beta-3


Mass: 333.365 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: The RGT peptide was synthesized in the solid phase / Source: (synth.) Homo sapiens (human) / References: UniProt: P05106
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 95 / 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: 1.73 Å3/Da / Density % sol: 28.79 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 100mM Tris, pH 8.0, 1.3M sodium citrate, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97885 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 30, 2010
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97885 Å / Relative weight: 1
ReflectionResolution: 2→29.2 Å / Num. all: 6533 / Num. obs: 6468 / % possible obs: 99 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 8 % / Biso Wilson estimate: 9.5 Å2 / Rmerge(I) obs: 0.17 / Rsym value: 0.17 / Net I/σ(I): 10
Reflection shellResolution: 2→2.08 Å / Redundancy: 8 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 7 / Num. unique all: 923 / Rsym value: 0.36 / % possible all: 100

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Processing

Software
NameVersionClassification
DNAdata collection
PHASERphasing
PHENIX(phenix.refine)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1FMK

1fmk


Resolution: 2→29.163 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8867 / SU ML: 0.22 / σ(F): 0.12 / Phase error: 18.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1925 614 9.8 %eRfree calculated using 10% of total reflections omitted from refinement.
Rwork0.1391 ---
obs0.1445 6144 98.92 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.425 Å2 / ksol: 0.402 e/Å3
Displacement parametersBiso max: 80.43 Å2 / Biso mean: 15.975 Å2 / Biso min: 1.64 Å2
Baniso -1Baniso -2Baniso -3
1-6.3265 Å2-0 Å2-3.684 Å2
2---5.8323 Å20 Å2
3----2.0635 Å2
Refinement stepCycle: LAST / Resolution: 2→29.163 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms945 0 0 95 1040
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007968
X-RAY DIFFRACTIONf_angle_d1.0251321
X-RAY DIFFRACTIONf_dihedral_angle_d16.389318
X-RAY DIFFRACTIONf_chiral_restr0.075147
X-RAY DIFFRACTIONf_plane_restr0.003167
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.0003-2.08040.20851350.1349121798
2.0804-2.1750.19371540.1406121398
2.175-2.28960.21541190.1356124798
2.2896-2.4330.22031240.1486123799
2.433-2.62080.21191520.1576122799
2.6208-2.88430.21641300.143124399
2.8843-3.30120.17871310.12571245100
3.3012-4.15720.14881330.11941247100
4.1572-29.16580.17791300.1496124599
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)
10.05310.0434-0.0760.3803-0.09830.20760.0162-0.0076-0.03250.011-0.05210.0651-0.00930.02380.02370.0120.0089-0.00090.0265-0.00580.03646.6441-9.213925.3687
20.07920.12680.22090.28170.28310.8886-0.0214-0.00210.0147-0.0111-0.05080.0334-0.02390.039-0.22040.01270.00940.00950.03170.00630.017214.0201-25.139637.8538
30.07460.0277-0.0570.2099-0.11010.1818-0.0134-0.0267-0.0083-0.0138-0.04260.00240.01490.03880.0350.5735-0.06660.09310.6742-0.03040.780715.7251-16.893918.1511
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain AA82 - 141
2X-RAY DIFFRACTION2chain BB83 - 141
3X-RAY DIFFRACTION3chain CC760 - 762

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