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- PDB-7aty: Solution NMR structure of the SH3 domain of human Caskin1 -

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Basic information

Entry
Database: PDB / ID: 7aty
TitleSolution NMR structure of the SH3 domain of human Caskin1
ComponentsCaskin-1
KeywordsSIGNALING PROTEIN / Caskin1 / SH3 domain / protein-lipid interaction / lipid signaling / proline-rich motif
Function / homology
Function and homology information


signal transduction / identical protein binding / cytoplasm
Similarity search - Function
Caskin-1, SH3 domain / Caskin, C-terminal / Caskin-1, CASK-interaction domain / Caskin1/2, SAM repeat 1 / Caskin1/2, SAM repeat 2 / Caskin1 CASK-interaction domain / C-terminal region of Caskin / Proline rich region of Caskin proteins / : / Variant SH3 domain ...Caskin-1, SH3 domain / Caskin, C-terminal / Caskin-1, CASK-interaction domain / Caskin1/2, SAM repeat 1 / Caskin1/2, SAM repeat 2 / Caskin1 CASK-interaction domain / C-terminal region of Caskin / Proline rich region of Caskin proteins / : / Variant SH3 domain / SAM domain (Sterile alpha motif) / Ankyrin repeats (many copies) / SAM domain profile. / Sterile alpha motif. / Sterile alpha motif domain / Sterile alpha motif/pointed domain superfamily / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsToke, O. / Koprivanacz, K. / Radnai, L. / Mero, B. / Juhasz, T. / Liliom, K. / Buday, L.
Funding support Hungary, 2items
OrganizationGrant numberCountry
National Research Development and Innovation Office (NKFIH)K82092 Hungary
National Research Development and Innovation Office (NKFIH)K109035 Hungary
Citation
Journal: Cells / Year: 2021
Title: Solution NMR Structure of the SH3 Domain of Human Caskin1 Validates the Lack of a Typical Peptide Binding Groove and Supports a Role in Lipid Mediator Binding.
Authors: Toke, O. / Koprivanacz, K. / Radnai, L. / Mero, B. / Juhasz, T. / Liliom, K. / Buday, L.
#1: Journal: Cell Signal / Year: 2017
Title: The SH3 domain of Caskin1 binds to lysophosphatidic acid suggesting a direct role for the lipid in intracellular signaling.
Authors: Koprivanacz, K. / Toke, O. / Besztercei, B. / Juhasz, T. / Radnai, L. / Mero, B. / Mihaly, J. / Peter, M. / Balogh, G. / Vigh, L. / Buday, L. / Liliom, K.
History
DepositionNov 1, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 3, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.2Jun 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

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Assembly

Deposited unit
A: Caskin-1


Theoretical massNumber of molelcules
Total (without water)7,4581
Polymers7,4581
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering, NMR relaxation study
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area4700 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)30 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Caskin-1 / CASK-interacting protein 1


Mass: 7458.308 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Residues 1-4 (GSHM) are from the expression tag. / Source: (gene. exp.) Homo sapiens (human) / Gene: CASKIN1, KIAA1306 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8WXD9

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
114isotropic12D 1H-15N HSQC
124isotropic13D HN(CA)CB
134isotropic13D CBCA(CO)NH
144isotropic13D HBHA(CO)NH
154isotropic13D CC-TOCSY-NNH
164isotropic13D HCC-TOCSY
174isotropic13D (H)CCH-TOCSY
184isotropic12D 1H-13C HSQC aliphatic
194isotropic12D 1H-13C HSQC aromatic
1105isotropic12D 1H-15N HSQC
1115isotropic12D 1H-15N HSQC NH2 only
1125isotropic13D 1H-15N NOESY
1134isotropic13D 1H-13C NOESY aliphatic
1144isotropic13D 1H-13C NOESY aromatic
1154isotropic13D Met-Met NOESY
1166isotropic12D 1H-1H NOESY

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Sample preparation

Details
TypeSolution-IDContentsDetailsLabelSolvent system
solution40.6 mM [U-13C; U-15N] human caskin1 SH3 domain, 90% H2O/10% D2O20 mM K-phosphate, 100 mM KCl, 0.05% NaN3, 0.1 mM TCEP, pH 7.213C_15N_sample90% H2O/10% D2O
solution50.6 mM [U-15N] human caskin1 SH3 domain, 90% H2O/10% D2O20 mM K-phosphate, 100 mM KCl, 0.05% NaN3, 0.1 mM TCEP, pH 7.215N_sample90% H2O/10% D2O
solution61 mM human caskin1 SH3 domain, 90% H2O/10% D2O20 mM K-phosphate, 100 mM KCl, 0.05% NaN3, 0.1 mM TCEP, pH 7.2unlabeled_sample90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.6 mMhuman caskin1 SH3 domain[U-13C; U-15N]4
0.6 mMhuman caskin1 SH3 domain[U-15N]5
1 mMhuman caskin1 SH3 domainnatural abundance6
Sample conditionsDetails: 20 mM K-phosphate, 100 mM KCl, 0.05% NaN3, 0.1 mM TCEP, pH 7.2
Ionic strength: 20 mM K-phosphate, 100 mM KCl, 0.05% NaN3, 0.1 mM TCEP Not defined
Label: condition_1 / pH: 7.2 / PH err: 0.1 / Pressure: 1 atm / Temperature: 283 K / Temperature err: 0.1

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NMR measurement

NMR spectrometerType: Varian Uniform NMR System / Manufacturer: Varian / Model: Uniform NMR System / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
VnmrJVariancollection
FelixAccelrys Software Inc.chemical shift assignment
FelixAccelrys Software Inc.peak picking
ARIALinge, O'Donoghue and Nilgesstructure calculation
ARIALinge, O'Donoghue and Nilgesrefinement
RefinementMethod: simulated annealing / Software ordinal: 5
Details: torsional angle simulated annealing followed by torsional angle and Cartesian molecular dynamics cooling stages
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 30

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