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- PDB-5o99: Unconventional SH3 domain from the postsynaptic density scaffold ... -

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Basic information

Entry
Database: PDB / ID: 5o99
TitleUnconventional SH3 domain from the postsynaptic density scaffold protein Shank3
ComponentsSH3 and multiple ankyrin repeat domains protein 3
KeywordsPROTEIN BINDING / postsynaptic density / scaffolding protein / SH3 domain / non-canonical binding site
Function / homology
Function and homology information


response to interleukin-17 / regulation of AMPA glutamate receptor clustering / guanylate kinase-associated protein clustering / striatal medium spiny neuron differentiation / synaptic receptor adaptor activity / RET signaling / postsynaptic density assembly / embryonic epithelial tube formation / positive regulation of synapse structural plasticity / vocal learning ...response to interleukin-17 / regulation of AMPA glutamate receptor clustering / guanylate kinase-associated protein clustering / striatal medium spiny neuron differentiation / synaptic receptor adaptor activity / RET signaling / postsynaptic density assembly / embryonic epithelial tube formation / positive regulation of synapse structural plasticity / vocal learning / Neurexins and neuroligins / negative regulation of actin filament bundle assembly / structural constituent of postsynaptic density / regulation of grooming behavior / positive regulation of long-term neuronal synaptic plasticity / NMDA glutamate receptor clustering / vocalization behavior / negative regulation of cell volume / regulation of behavioral fear response / neuron spine / positive regulation of glutamate receptor signaling pathway / AMPA glutamate receptor clustering / regulation of dendritic spine morphogenesis / dendritic spine morphogenesis / locomotion / brain morphogenesis / regulation of long-term synaptic potentiation / regulation of postsynapse organization / neural precursor cell proliferation / long-term synaptic depression / exploration behavior / ciliary membrane / positive regulation of dendritic spine development / regulation of long-term synaptic depression / social behavior / adult behavior / associative learning / locomotory exploration behavior / neuromuscular process controlling balance / positive regulation of excitatory postsynaptic potential / postsynaptic density, intracellular component / glial cell proliferation / synapse assembly / ionotropic glutamate receptor binding / positive regulation of synaptic transmission, glutamatergic / learning / positive regulation of long-term synaptic potentiation / locomotory behavior / G protein-coupled receptor binding / modulation of chemical synaptic transmission / regulation of synaptic plasticity / SH3 domain binding / memory / long-term synaptic potentiation / MAPK cascade / actin binding / scaffold protein binding / gene expression / dendritic spine / learning or memory / neuron projection / postsynaptic density / protein-containing complex binding / glutamatergic synapse / zinc ion binding / identical protein binding / plasma membrane / cytoplasm
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 / Ankyrin repeat-containing domain superfamily / Src homology 3 domains / SH3 type barrels. / 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 speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 0.871 Å
AuthorsPonna, S.K. / Myllykoski, M. / Boeckers, T.M. / Kursula, P.
Funding support Finland, 2items
OrganizationGrant numberCountry
Sigrid Juselius Foundation Finland
Emil Aaltonen Foundation Finland
CitationJournal: Biochem. Biophys. Res. Commun. / Year: 2017
Title: Structure of an unconventional SH3 domain from the postsynaptic density protein Shank3 at ultrahigh resolution.
Authors: Ponna, S.K. / Myllykoski, M. / Boeckers, T.M. / Kursula, P.
History
DepositionJun 16, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 5, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 2, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_id_ASTM ..._citation.country / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2May 8, 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
B: SH3 and multiple ankyrin repeat domains protein 3
A: SH3 and multiple ankyrin repeat domains protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,0923
Polymers12,8832
Non-polymers2091
Water4,089227
1
B: SH3 and multiple ankyrin repeat domains protein 3


Theoretical massNumber of molelcules
Total (without water)6,4411
Polymers6,4411
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
A: SH3 and multiple ankyrin repeat domains protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,6512
Polymers6,4411
Non-polymers2091
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)29.740, 52.910, 31.660
Angle α, β, γ (deg.)90.00, 90.05, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 6441.268 Da / Num. of mol.: 2 / Fragment: UNP residues 470-528
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Shank3, Prosap2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9JLU4
#2: Chemical ChemComp-BTB / 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / BIS-TRIS BUFFER


Mass: 209.240 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H19NO5 / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 227 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.93 Å3/Da / Density % sol: 36.39 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M bis-tris (pH 6.5), 32.5% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.977 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 23, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.977 Å / Relative weight: 1
ReflectionResolution: 0.87→50 Å / Num. obs: 64681 / % possible obs: 81 % / Redundancy: 3.5 % / Biso Wilson estimate: 9.2 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.037 / Net I/σ(I): 20.9
Reflection shellResolution: 0.87→0.89 Å / Redundancy: 2 % / Rmerge(I) obs: 0.395 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 698 / CC1/2: 0.757 / % possible all: 11.8

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Processing

Software
NameVersionClassification
PHENIX(1.12rc1_2801: ???)refinement
XDSdata reduction
XDSdata scaling
Auto-Rickshawphasing
RefinementMethod to determine structure: SAD / Resolution: 0.871→29.74 Å / Cross valid method: FREE R-VALUE / σ(F): 1.27 / Phase error: 17.5 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.1173 1421 2.2 %
Rwork0.0971 --
obs0.112 64681 80.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 0.871→29.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms900 0 14 227 1141
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.019988
X-RAY DIFFRACTIONf_angle_d1.4721339
X-RAY DIFFRACTIONf_dihedral_angle_d17.236370
X-RAY DIFFRACTIONf_chiral_restr0.117131
X-RAY DIFFRACTIONf_plane_restr0.009176
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
0.875-0.91010.339380.40351862X-RAY DIFFRACTION21
0.9101-0.95150.2597960.24414661X-RAY DIFFRACTION53
0.9515-1.00170.15491510.15957401X-RAY DIFFRACTION85
1.0017-1.06440.13371600.12547880X-RAY DIFFRACTION89
1.0644-1.14660.12531620.1127912X-RAY DIFFRACTION91
1.1466-1.2620.12741680.11438216X-RAY DIFFRACTION94
1.262-1.44460.12991710.11548409X-RAY DIFFRACTION96
1.4446-1.820.12341730.10768460X-RAY DIFFRACTION96
1.82-27.18080.13071750.09268556X-RAY DIFFRACTION96

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