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- PDB-2l1c: Shc-PTB:biphosphorylated integrin beta3 cytoplasmic tail complex (1:1) -

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Basic information

Entry
Database: PDB / ID: 2l1c
TitleShc-PTB:biphosphorylated integrin beta3 cytoplasmic tail complex (1:1)
Components
  • Integrin beta-3
  • SHC (Src homology 2 domain containing) transforming protein 1, isoform CRA_d
KeywordsCELL ADHESION / Shc-PTB / integrin beta3 / cytoplasmic tail
Function / homology
Function and homology information


regulation of superoxide metabolic process / positive regulation of cell proliferation in bone marrow / tube development / regulation of serotonin uptake / positive regulation of adenylate cyclase-inhibiting opioid receptor signaling pathway / alpha9-beta1 integrin-ADAM8 complex / regulation of trophoblast cell migration / integrin alphaIIb-beta3 complex / regulation of postsynaptic neurotransmitter receptor diffusion trapping / maintenance of postsynaptic specialization structure ...regulation of superoxide metabolic process / positive regulation of cell proliferation in bone marrow / tube development / regulation of serotonin uptake / positive regulation of adenylate cyclase-inhibiting opioid receptor signaling pathway / alpha9-beta1 integrin-ADAM8 complex / regulation of trophoblast cell migration / integrin alphaIIb-beta3 complex / regulation of postsynaptic neurotransmitter receptor diffusion trapping / maintenance of postsynaptic specialization structure / alphav-beta3 integrin-vitronectin complex / regulation of extracellular matrix organization / XBP1(S) activates chaperone genes / positive regulation of glomerular mesangial cell proliferation / platelet alpha granule membrane / negative regulation of lipoprotein metabolic process / integrin alphav-beta3 complex / neurotrophin TRKA receptor binding / alphav-beta3 integrin-PKCalpha complex / fibrinogen binding / alphav-beta3 integrin-HMGB1 complex / blood coagulation, fibrin clot formation / glycinergic synapse / vascular endothelial growth factor receptor 2 binding / negative regulation of lipid transport / transmembrane receptor protein tyrosine kinase adaptor activity / positive regulation of vascular endothelial growth factor signaling pathway / : / regulation of release of sequestered calcium ion into cytosol / Elastic fibre formation / mesodermal cell differentiation / Interleukin-15 signaling / cell-substrate junction assembly / alphav-beta3 integrin-IGF-1-IGF1R complex / platelet-derived growth factor receptor binding / angiogenesis involved in wound healing / filopodium membrane / extracellular matrix binding / positive regulation of fibroblast migration / Interleukin-2 signaling / positive regulation of vascular endothelial growth factor receptor signaling pathway / regulation of bone resorption / apolipoprotein A-I-mediated signaling pathway / positive regulation of cell adhesion mediated by integrin / Signaling by LTK / apoptotic cell clearance / wound healing, spreading of epidermal cells / integrin complex / heterotypic cell-cell adhesion / Shc-EGFR complex / epidermal growth factor receptor binding / smooth muscle cell migration / Molecules associated with elastic fibres / epidermal growth factor binding / Mechanical load activates signaling by PIEZO1 and integrins in osteocytes / positive regulation of cell-matrix adhesion / Signaling by ALK / negative chemotaxis / cell adhesion mediated by integrin / cellular response to insulin-like growth factor stimulus / Syndecan interactions / microvillus membrane / p130Cas linkage to MAPK signaling for integrins / positive regulation of smooth muscle cell migration / regulation of postsynaptic neurotransmitter receptor internalization / protein disulfide isomerase activity / cell-substrate adhesion / positive regulation of osteoblast proliferation / PECAM1 interactions / TGF-beta receptor signaling activates SMADs / GRB2:SOS provides linkage to MAPK signaling for Integrins / lamellipodium membrane / platelet-derived growth factor receptor signaling pathway / fibronectin binding / negative regulation of macrophage derived foam cell differentiation / RET signaling / negative regulation of lipid storage / Interleukin-3, Interleukin-5 and GM-CSF signaling / Activated NTRK3 signals through RAS / Activated NTRK2 signals through RAS / SHC1 events in ERBB4 signaling / Role of LAT2/NTAL/LAB on calcium mobilization / Signalling to RAS / ECM proteoglycans / Interleukin receptor SHC signaling / Integrin cell surface interactions / positive regulation of bone resorption / Signal attenuation / SHC-related events triggered by IGF1R / positive regulation of T cell migration / SHC-mediated cascade:FGFR3 / negative regulation of endothelial cell apoptotic process / MET activates RAS signaling / SHC-mediated cascade:FGFR2 / SHC-mediated cascade:FGFR4 / Signaling by CSF3 (G-CSF) / Erythropoietin activates RAS / SHC-mediated cascade:FGFR1 / coreceptor activity / cell adhesion molecule binding
Similarity search - Function
Phosphotyrosine interaction domain, Shc-like / SH2 adaptor protein C, SH2 domain / : / Phosphotyrosine interaction domain (PTB/PID) / Phosphotyrosine interaction domain (PID) profile. / Phosphotyrosine-binding domain, phosphotyrosine-interaction (PI) domain / PTB/PI domain / Integrin beta, epidermal growth factor-like domain 1 / Integrin beta epidermal growth factor like domain 1 / Integrin beta subunit, cytoplasmic domain ...Phosphotyrosine interaction domain, Shc-like / SH2 adaptor protein C, SH2 domain / : / Phosphotyrosine interaction domain (PTB/PID) / Phosphotyrosine interaction domain (PID) profile. / Phosphotyrosine-binding domain, phosphotyrosine-interaction (PI) domain / PTB/PI 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 EGF domain / Integrin beta subunit, tail / Integrin beta tail domain superfamily / Integrin_B_tail / EGF-like domain, extracellular / EGF-like domain / Integrins beta chain EGF (I-EGF) domain profile. / Integrin beta subunit, VWA domain / Integrin beta subunit / Integrin beta N-terminal / Integrin beta chain VWA domain / Integrin plexin domain / Integrins beta chain EGF (I-EGF) domain signature. / Integrin beta subunits (N-terminal portion of extracellular region) / Integrin domain superfamily / PSI domain / domain found in Plexins, Semaphorins and Integrins / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / von Willebrand factor A-like domain superfamily / EGF-like domain signature 1. / EGF-like domain signature 2. / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / SH2 domain superfamily / PH-like domain superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
SHC-transforming protein 1 / Integrin beta-3 / SHC-transforming protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / DGSA-distance geometry simulated annealing
Model detailsclosest to the average, model 1
AuthorsDeshmukh, L. / Gorbatyuk, V. / Vinogradova, O.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: Integrin {beta}3 phosphorylation dictates its complex with the Shc phosphotyrosine-binding (PTB) domain.
Authors: Deshmukh, L. / Gorbatyuk, V. / Vinogradova, O.
History
DepositionJul 27, 2010Deposition site: BMRB / Processing site: RCSB
Revision 1.0Aug 18, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 18, 2012Group: Database references
Revision 1.3Oct 9, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_nmr_software / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SHC (Src homology 2 domain containing) transforming protein 1, isoform CRA_d
B: Integrin beta-3


Theoretical massNumber of molelcules
Total (without water)26,4522
Polymers26,4522
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)15 / 80structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein SHC (Src homology 2 domain containing) transforming protein 1, isoform CRA_d


Mass: 23167.484 Da / Num. of mol.: 1 / Fragment: PTB domain (UNP residues 17-207)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SHC1, hCG_1997126 / Production host: Escherichia coli (E. coli) / References: UniProt: D3DV78, UniProt: P29353*PLUS
#2: Protein/peptide Integrin beta-3 / Platelet membrane glycoprotein IIIa / GPIIIa


Mass: 3284.377 Da / Num. of mol.: 1 / Fragment: UNP residues 762-788 / Source method: obtained synthetically
Details: The peptide was chemically synthesized based on the sequence of the human integrin beta3 cytoplasmic tail (representing residues 736R-762G)
References: UniProt: P05106
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1313D HNCO
1413D HNCA
1513D HN(CA)CB
1613D HBHA(CO)NH
1713D 1H-15N edited NOESY
1813D 1H-13C edited NOESY
1913D HN(CA)CO
11013D 1H-13C aromatic NOESY
11112D 13C,15N FilteredTOCSY
11212D 13C,15N Filtered NOESY
11313D F1 13C,15N Filtered, F2 13C edited NOESY-HSQC

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Sample preparation

DetailsContents: 0.4 mM [U-99% 13C; U-99% 15N] Shc, 0.8 mM integrin beta3, 5 mM DTT, 50 mM sodium chloride, 50 mM sodium phosphate, 1 mM DSS, 93% H2O/7% D2O
Solvent system: 93% H2O/7% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.4 mMentity_1-1[U-99% 13C; U-99% 15N]1
0.8 mMentity_2-21
5 mMDTT-31
50 mMsodium chloride-41
50 mMsodium phosphate-51
1 mMDSS-61
Sample conditionspH: 6.5 / Pressure: ambient / Temperature: 308 K

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
CNS1.21Brunger, Adams, Clore, Gros, Nilges and Readrefinement
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
VnmrJVariancollection
CCPN-Analysis2.1.3(CCPN-Analysis)-Vranken,Boucher, Stevens, Fogh, Pajon,Llinas,Ulrich,Markley,Ionides,Lauedata analysis
CCPN-Analysis2.1.3(CCPN-Analysis)-Vranken,Boucher, Stevens, Fogh, Pajon,Llinas,Ulrich,Markley,Ionides,Lauepeak picking
RefinementMethod: DGSA-distance geometry simulated annealing / Software ordinal: 1 / Details: refinement in explicit water
NMR constraintsNOE constraints total: 4196 / NOE intraresidue total count: 1793 / NOE medium range total count: 1704 / NOE sequential total count: 699 / Hydrogen bond constraints total count: 166
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 80 / Conformers submitted total number: 15

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