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- PDB-7pll: Structure of the murine cortactin C-SH3 domain in complex with a ... -

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Basic information

Entry
Database: PDB / ID: 7pll
TitleStructure of the murine cortactin C-SH3 domain in complex with a Pyk2 proline-rich ligand
Components
  • Pyk2-PRR2 peptide
  • Src substrate cortactin
KeywordsCELL INVASION / SH3 domain / cortactin / Pyk2 / signaling / cancer
Function / homology
Function and homology information


lamellipodium organization / site of polarized growth / Arp2/3 complex binding / modification of postsynaptic actin cytoskeleton / modification of postsynaptic structure / mitotic spindle midzone / regulation of cell projection assembly / regulation of mitophagy / profilin binding / postsynaptic actin cytoskeleton ...lamellipodium organization / site of polarized growth / Arp2/3 complex binding / modification of postsynaptic actin cytoskeleton / modification of postsynaptic structure / mitotic spindle midzone / regulation of cell projection assembly / regulation of mitophagy / profilin binding / postsynaptic actin cytoskeleton / positive regulation of smooth muscle contraction / regulation of actin filament polymerization / positive regulation of chemotaxis / substrate-dependent cell migration, cell extension / focal adhesion assembly / podosome / proline-rich region binding / dendritic spine maintenance / regulation of axon extension / cortical actin cytoskeleton / positive regulation of actin filament polymerization / cortical cytoskeleton / neuron projection morphogenesis / extrinsic apoptotic signaling pathway / clathrin-coated pit / voltage-gated potassium channel complex / ruffle / receptor-mediated endocytosis / negative regulation of extrinsic apoptotic signaling pathway / actin filament / cell motility / intracellular protein transport / actin filament binding / cell junction / cell migration / lamellipodium / cell cortex / actin cytoskeleton organization / postsynapse / dendritic spine / focal adhesion / glutamatergic synapse / Golgi apparatus / endoplasmic reticulum / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Hs1/Cortactin / Cortactin, SH3 domain / Repeat in HS1/Cortactin / Cortactin repeat profile. / Variant SH3 domain / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain
Similarity search - Domain/homology
Src substrate cortactin
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodSOLUTION NMR / DGSA-distance geometry simulated annealing
AuthorsSokolik, C.G. / Samson, A.O. / Gil-Henn, H. / Chill, J.H.
Funding support Israel, 1items
OrganizationGrant numberCountry
Israel Science Foundation964/19 Israel
Citation
Journal: Oncogene / Year: 2023
Title: A novel Pyk2-derived peptide inhibits invadopodia-mediated breast cancer metastasis.
Authors: Twafra, S. / Sokolik, C.G. / Sneh, T. / Srikanth, K.D. / Meirson, T. / Genna, A. / Chill, J.H. / Gil-Henn, H.
#1: Journal: Biorxiv / Year: 2022
Title: A novel Pyk2-derived peptide inhibits invadopodia-mediated breast cancer metastasis
Authors: Twafra, S. / Sokolik, C.G. / Sneh, T. / Srikanth, K.D. / Meirson, T. / Genna, A. / Chill, J.H. / Gil-Henn, H.
History
DepositionAug 31, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 13, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 2, 2022Group: Database references / Category: citation / citation_author
Revision 1.2Feb 1, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.3Jun 14, 2023Group: Other / Category: pdbx_database_status / Item: _pdbx_database_status.status_code_nmr_data
Revision 1.4Jun 19, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Src substrate cortactin
B: Pyk2-PRR2 peptide


Theoretical massNumber of molelcules
Total (without water)8,9972
Polymers8,9972
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area1080 Å2
ΔGint-3 kcal/mol
Surface area5560 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein Src substrate cortactin


Mass: 6802.532 Da / Num. of mol.: 1 / Fragment: SH3 domain, UNP Residues 490-546
Source method: isolated from a genetically manipulated source
Details: murine sequence of cortactin SH3 domain / Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cttn, Ems1 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q60598
#2: Protein/peptide Pyk2-PRR2 peptide


Mass: 2194.530 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
113isotropic12D 1H-1H TOCSY
123isotropic12D 1H-1H NOESY
133isotropic11H-15N HSQC
143isotropic13D HN(CA)CB
155isotropic12D 1H-1H TOCSY
165isotropic12D 1H-1H NOESY
175isotropic12D 1H-1H COSY
185isotropic13D 12C13C filtered-edited NOESY
193isotropic12D 1H-1H TOCSY
1103isotropic12D 1H-1H NOESY
1116isotropic12D 1H-1H TOCSY
1126isotropic12D 1H-1H NOESY
1134isotropic12D 1H-1H TOCSY

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Sample preparation

Details
TypeSolution-IDContentsDetailsLabelSolvent system
solution30.8 mM cortactin C-terminal SH3 domain, 0.8 mM Pyk2-PRR2 peptide, 30 mM sodium phosphate, 0.01 % w/v sodium azide, 93% H2O/7% D2Ounlabeled SH3 in complex with PRR2complex_393% H2O/7% D2O
solution40.5 mM Pyk2-PRR2 peptide, 30 mM sodium phosphate, 0.01 % w/v sodium azide, 93% H2O/7% D2Ounlabeled PRR2peptide_only93% H2O/7% D2O
solution50.8 mM 2H,13C,15N cortactin C-terminal SH3 domain, 0.8 mM Pyk2-PRR2 peptide, 30 mM sodium phosphate, 0.01 % w/v sodium azide, 100% D2ODCN-SH3 in complex with PRR2complex_1_D2O100% D2O
solution60.8 mM cortactin C-terminal SH3 domain, 0.8 mM Pyk2-PRR2 peptide, 30 mM sodium phosphate, 0.01 % w/v sodium azide, 100% D2Ounlabeled SH3 in complex with PRR2complex_3_D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.8 mMcortactin C-terminal SH3 domainnone3
0.8 mMPyk2-PRR2 peptidenone3
30 mMsodium phosphatenone3
0.01 % w/vsodium azidenone3
0.5 mMPyk2-PRR2 peptidenone4
30 mMsodium phosphatenone4
0.01 % w/vsodium azidenone4
0.8 mMcortactin C-terminal SH3 domain2H,13C,15N5
0.8 mMPyk2-PRR2 peptidenone5
30 mMsodium phosphatenone5
0.01 % w/vsodium azidenone5
0.8 mMcortactin C-terminal SH3 domainnone6
0.8 mMPyk2-PRR2 peptidenone6
30 mMsodium phosphatenone6
0.01 % w/vsodium azidenone6
Sample conditionsIonic strength: 123 mM / Ionic strength err: 2 / Label: conditions_1 / pH: 6.5 / PH err: 0.1 / Pressure: 1 atm / Pressure err: 0 / Temperature: 296 K / Temperature err: 0.5

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NMR measurement

NMR spectrometerType: Bruker DRX700 / Manufacturer: Bruker / Model: DRX700 / Field strength: 700 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CNS1.3Brunger, Adams, Clore, Gros, Nilges and Readstructure calculation
TALOS+Shen, Grishaev, Baxstructure calculation
TopSpin3.6.1Bruker Biospinchemical shift assignment
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
TopSpin3.6.1Bruker Biospinpeak picking
RefinementMethod: DGSA-distance geometry simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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