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- PDB-9ezn: Canonical class 1 structure of the human cortactin SH3 domain in ... -

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Basic information

Entry
Database: PDB / ID: 9ezn
TitleCanonical class 1 structure of the human cortactin SH3 domain in complex with WIP-derived peptide
Components
  • WAS/WASL-interacting protein family member 1
  • cDNA FLJ34459 fis, clone HLUNG2002916, highly similar to SRC SUBSTRATE CORTACTIN
KeywordsSIGNALING PROTEIN / SH3 domain / cortactin / WASp-interacting protein (WIP) / cytoskeletal regulation / cortactin-WIP complex
Function / homology
Function and homology information


profilin binding / actin filament-based movement / cytoskeletal anchor activity / response to other organism / actin polymerization or depolymerization / podosome / CDC42 GTPase cycle / RHO GTPases Activate WASPs and WAVEs / ruffle / clathrin-coated pit ...profilin binding / actin filament-based movement / cytoskeletal anchor activity / response to other organism / actin polymerization or depolymerization / podosome / CDC42 GTPase cycle / RHO GTPases Activate WASPs and WAVEs / ruffle / clathrin-coated pit / RAC1 GTPase cycle / protein folding chaperone / FCGR3A-mediated phagocytosis / actin filament / Regulation of actin dynamics for phagocytic cup formation / SH3 domain binding / endocytosis / lamellipodium / actin cytoskeleton / actin binding / protein-containing complex assembly / cytoplasmic vesicle / cell cortex / dendritic spine / focal adhesion / endoplasmic reticulum / plasma membrane / cytosol
Similarity search - Function
: / Cortactin, SH3 domain / Wiskott Aldrich syndrome homology region 2 / WH2 motif / WH2 domain profile. / WH2 domain / Variant SH3 domain / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. ...: / Cortactin, SH3 domain / Wiskott Aldrich syndrome homology region 2 / WH2 motif / WH2 domain profile. / WH2 domain / Variant SH3 domain / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / PH-like domain superfamily
Similarity search - Domain/homology
Src substrate cortactin / WAS/WASL-interacting protein family member 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsSokolik, C.G. / Chill, J.H.
Funding support Israel, 1items
OrganizationGrant numberCountry
Israel Science Foundation964/19 Israel
CitationJournal: J.Mol.Biol. / Year: 2025
Title: A Triple-pose Complex Between an Extended WIP Motif and a C-terminal SH3 Domain Modulates Cortactin Activity.
Authors: Sokolik, C.G. / Chill, J.H.
History
DepositionApr 13, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 19, 2025Provider: repository / Type: Initial release
Revision 1.1Feb 26, 2025Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: cDNA FLJ34459 fis, clone HLUNG2002916, highly similar to SRC SUBSTRATE CORTACTIN
B: WAS/WASL-interacting protein family member 1


Theoretical massNumber of molelcules
Total (without water)8,6142
Polymers8,6142
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: NMR Distance Restraints, not applicable, NMR relaxation study
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area870 Å2
ΔGint-2 kcal/mol
Surface area5900 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with acceptable covalent geometry
RepresentativeModel #1lowest energy

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Components

#1: Protein cDNA FLJ34459 fis, clone HLUNG2002916, highly similar to SRC SUBSTRATE CORTACTIN


Mass: 6462.111 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET-28-a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): T7Express / References: UniProt: B3KRK4
#2: Protein/peptide WAS/WASL-interacting protein family member 1 / Protein PRPL-2 / Wiskott-Aldrich syndrome protein-interacting protein / WASP-interacting protein


Mass: 2151.449 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: O43516
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-1H TOCSY
122isotropic12D 1H-1H TOCSY
133isotropic12D 1H-1H TOCSY
143isotropic12D 1H-1H NOESY
153isotropic12D 1H-15N HSQC
164isotropic12D 1H-1H TOCSY
174isotropic12D 1H-1H NOESY
184isotropic12D 1H-1H COSY
195isotropic13D 13C-filtered-12C-edited NOESY-HSQC

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution10.7 mM Human WIP (165-183), 20 mM potassium phosphate, 20 mM sodium chloride, 0.02 % sodium azide, 93% H2O/7% D2OWIPu H2O93% H2O/7% D2O
solution20.7 mM Human WIP (165-183), 20 mM potassium phosphate, 20 mM sodium chloride, 0.02 % sodium azide, 100% D2OWIPu D2O100% D2O
solution31.1 mM Human WIP (165-183), 0.22 mM [U-99% 15N; U-80% 2H] Human cortactin SH3 domain (494-550), 20 mM potassium phosphate, 20 mM sodium chloride, 1 mM dithiothreitol, 0.02 % sodium azide, 93% H2O/7% D2O2H15N SH3-WIPu H2O93% H2O/7% D2O
solution41.1 mM Human WIP (165-183), 0.22 mM [U-99% 15N; U-80% 2H] Human cortactin SH3 domain (494-550), 20 mM potassium phosphate, 20 mM sodium chloride, 1 mM dithiothreitol, 0.02 % sodium azide, 100% D2O2H15N SH3-WIPu D2O100% D2O
solution51.1 mM Human WIP (165-183), 0.22 mM [U-99% 13C; U-99% 15N] Human cortactin SH3 domain (494-550), 20 mM potassium phosphate, 20 mM sodium chloride, 1 mM dithiothreitol, 0.02 % sodium azide, 100% D2O13C15N SH3-WIPu D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.7 mMHuman WIP (165-183)natural abundance1
20 mMpotassium phosphatenatural abundance1
20 mMsodium chloridenatural abundance1
0.02 %sodium azidenatural abundance1
0.7 mMHuman WIP (165-183)natural abundance2
20 mMpotassium phosphatenatural abundance2
20 mMsodium chloridenatural abundance2
0.02 %sodium azidenatural abundance2
1.1 mMHuman WIP (165-183)natural abundance3
0.22 mMHuman cortactin SH3 domain (494-550)[U-99% 15N; U-80% 2H]3
20 mMpotassium phosphatenatural abundance3
20 mMsodium chloridenatural abundance3
1 mMdithiothreitolnatural abundance3
0.02 %sodium azidenatural abundance3
1.1 mMHuman WIP (165-183)natural abundance4
0.22 mMHuman cortactin SH3 domain (494-550)[U-99% 15N; U-80% 2H]4
20 mMpotassium phosphatenatural abundance4
20 mMsodium chloridenatural abundance4
1 mMdithiothreitolnatural abundance4
0.02 %sodium azidenatural abundance4
1.1 mMHuman WIP (165-183)natural abundance5
0.22 mMHuman cortactin SH3 domain (494-550)[U-99% 13C; U-99% 15N]5
20 mMpotassium phosphatenatural abundance5
20 mMsodium chloridenatural abundance5
1 mMdithiothreitolnatural abundance5
0.02 %sodium azidenatural abundance5
Sample conditionsDetails: 20 mM KPi, 20 mM NaCl, 1 mM DTT, 0.02% NaN3 / Ionic strength: 0.055 M / Ionic strength err: 0.001 / Label: conditions_1 / pH: 6.6 / PH err: 0.1 / Pressure: 1 atm / Pressure err: 0 / Temperature: 298 K / Temperature err: 0.1

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NMR measurement

NMR spectrometerType: Bruker AVANCE DRX / Manufacturer: Bruker / Model: AVANCE DRX / Field strength: 700 MHz

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin3.6.4Bruker Biospinchemical shift assignment
CNS1.3Brunger, Adams, Clore, Gros, Nilges and Readstructure calculation
CNS1.3Brunger, Adams, Clore, Gros, Nilges and Readrefinement
TopSpin3.6.4Bruker Biospinpeak picking
TALOS+Shen, Grishaev, Baxstructure calculation
TopSpin3.6.4Bruker Biospinprocessing
RefinementMethod: simulated annealing / Software ordinal: 3
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with acceptable covalent geometry
Conformers calculated total number: 100 / Conformers submitted total number: 20

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