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- PDB-6cpk: Solution structure of SH3 domain from Shank3 -

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Basic information

Entry
Database: PDB / ID: 6cpk
TitleSolution structure of SH3 domain from Shank3
ComponentsSH3 and multiple ankyrin repeat domains protein 3
KeywordsPROTEIN BINDING / PSD / scaffold protein / postsynaptic density
Function / homology
Function and homology information


guanylate kinase-associated protein clustering / positive regulation of synapse structural plasticity / striatal medium spiny neuron differentiation / synaptic receptor adaptor activity / postsynaptic density assembly / vocal learning / negative regulation of actin filament bundle assembly / negative regulation of cell volume / positive regulation of long-term neuronal synaptic plasticity / NMDA glutamate receptor clustering ...guanylate kinase-associated protein clustering / positive regulation of synapse structural plasticity / striatal medium spiny neuron differentiation / synaptic receptor adaptor activity / postsynaptic density assembly / vocal learning / negative regulation of actin filament bundle assembly / negative regulation of cell volume / positive regulation of long-term neuronal synaptic plasticity / NMDA glutamate receptor clustering / vocalization behavior / neuron spine / AMPA glutamate receptor clustering / positive regulation of glutamate receptor signaling pathway / regulation of dendritic spine morphogenesis / dendritic spine morphogenesis / brain morphogenesis / regulation of long-term synaptic potentiation / Neurexins and neuroligins / neuromuscular process controlling balance / ciliary membrane / positive regulation of dendritic spine development / adult behavior / RET signaling / social behavior / positive regulation of excitatory postsynaptic potential / positive regulation of synaptic transmission, glutamatergic / synapse assembly / regulation of long-term synaptic depression / ionotropic glutamate receptor binding / positive regulation of long-term synaptic potentiation / learning / SH3 domain binding / memory / MAPK cascade / actin binding / scaffold protein binding / dendritic spine / neuron projection / postsynaptic density / zinc ion binding / plasma membrane / cytosol
Similarity search - Function
: / PDZ domain 6 / PDZ domain / Variant SH3 domain / SAM domain (Sterile alpha motif) / SH3 Domains / SAM domain profile. / Sterile alpha motif. / Sterile alpha motif domain / Sterile alpha motif/pointed domain superfamily ...: / PDZ domain 6 / PDZ domain / Variant SH3 domain / SAM domain (Sterile alpha motif) / SH3 Domains / SAM domain profile. / Sterile alpha motif. / Sterile alpha motif domain / Sterile alpha motif/pointed domain superfamily / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / SH3 type barrels. / Ankyrin repeat-containing domain superfamily / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Roll / Mainly Beta
Similarity search - Domain/homology
SH3 and multiple ankyrin repeat domains protein 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsIshida, H. / Vogel, H.J.
Funding support Canada, 1items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada) Canada
CitationJournal: FEBS Lett. / Year: 2018
Title: Solution structures of the SH3 domains from Shank scaffold proteins and their interactions with Cav1.3 calcium channels.
Authors: Ishida, H. / Skorobogatov, A. / Yamniuk, A.P. / Vogel, H.J.
History
DepositionMar 13, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 15, 2018Provider: repository / Type: Initial release
Revision 1.1Sep 12, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 8, 2020Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / pdbx_nmr_spectrometer
Item: _pdbx_audit_support.funding_organization / _pdbx_nmr_spectrometer.model
Revision 1.3May 1, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SH3 and multiple ankyrin repeat domains protein 3


Theoretical massNumber of molelcules
Total (without water)6,6171
Polymers6,6171
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)25 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein SH3 and multiple ankyrin repeat domains protein 3 / Shank3 / Proline-rich synapse-associated protein 2 / ProSAP2


Mass: 6616.582 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SHANK3, KIAA1650, PROSAP2, PSAP2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9BYB0

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
113isotropic12D 1H-15N HSQC
121isotropic13D CBCA(CO)NH
131isotropic13D HN(CA)CB
141isotropic13D HNCO
151isotropic13D HN(CA)CO
181isotropic13D C(CO)NH
171isotropic13D H(CCO)NH
161isotropic13D HBHA(CO)NH
192isotropic13D 1H-13C NOESY
1113isotropic13D 1H-15N NOESY
1104isotropic12D NOESY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution11 mM [U-99% 13C; U-99% 15N] Shank3 SH3, 20 mM Bis-Tris, 100 mM KCl, 90% H2O/10% D2O13C,15N_sample90% H2O/10% D2O
solution21 mM [U-99% 13C; U-99% 15N] Shank3 SH3, 20 mM Bis-Tris, 100 mM KCl, 100% D2O13C,15N_sample2100% D2O
solution31 mM [U-99% 15N] Shank3 SH3, 20 mM Bis-Tris, 100 mM KCl, 90% H2O/10% D2O15N_sample90% H2O/10% D2O
solution41 mM Shank3 SH3, 20 mM Bis-Tris, 100 mM KCl, 100% D2Ounlabeled_sample100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMShank3 SH3[U-99% 13C; U-99% 15N]1
20 mMBis-Trisnatural abundance1
100 mMKClnatural abundance1
1 mMShank3 SH3[U-99% 13C; U-99% 15N]2
20 mMBis-Trisnatural abundance2
100 mMKClnatural abundance2
1 mMShank3 SH3[U-99% 15N]3
20 mMBis-Trisnatural abundance3
100 mMKClnatural abundance3
1 mMShank3 SH3natural abundance4
20 mMBis-Trisnatural abundance4
100 mMKClnatural abundance4
Sample conditionsIonic strength: 100 mM / Label: condition_1 / pH: 6.8 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 500 MHz

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRViewJohnson, One Moon Scientificdata analysis
CYANA2Guntert, Mumenthaler and Wuthrichstructure calculation
RefinementMethod: torsion angle dynamics / Software ordinal: 3
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 25

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