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- PDB-5ova: Apo PDZ domain from rat Shank3 -

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Basic information

Entry
Database: PDB / ID: 5ova
TitleApo PDZ domain from rat Shank3
ComponentsSH3 and multiple ankyrin repeat domains protein 3
KeywordsPROTEIN BINDING / PDZ domain / peptide binding / post-synaptic density
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 / maintenance of postsynaptic density structure / postsynaptic density assembly / embryonic epithelial tube formation / Neurexins and neuroligins ...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 / maintenance of postsynaptic density structure / postsynaptic density assembly / embryonic epithelial tube formation / Neurexins and neuroligins / positive regulation of synapse structural plasticity / vocal learning / negative regulation of actin filament bundle assembly / structural constituent of postsynaptic density / positive regulation of glutamate receptor signaling pathway / regulation of grooming behavior / negative regulation of cell volume / positive regulation of long-term neuronal synaptic plasticity / NMDA glutamate receptor clustering / vocalization behavior / regulation of behavioral fear response / neuron spine / regulation of dendritic spine morphogenesis / AMPA glutamate receptor clustering / dendritic spine morphogenesis / locomotion / brain morphogenesis / regulation of long-term synaptic potentiation / neural precursor cell proliferation / long-term synaptic depression / exploration behavior / ciliary membrane / regulation of postsynapse organization / regulation of long-term synaptic depression / positive regulation of dendritic spine development / adult behavior / locomotory exploration behavior / associative learning / social 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 / long-term synaptic potentiation / modulation of chemical synaptic transmission / regulation of synaptic plasticity / memory / SH3 domain binding / MAPK cascade / actin binding / gene expression / scaffold protein binding / dendritic spine / postsynaptic density / learning or memory / neuron projection / glutamatergic synapse / protein-containing complex binding / 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) / PDZ domain / Pdz3 Domain / SAM domain profile. / Sterile alpha motif. / Sterile alpha motif domain ...: / PDZ domain 6 / PDZ domain / Variant SH3 domain / SAM domain (Sterile alpha motif) / PDZ domain / Pdz3 Domain / 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-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 / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsPonna, S.K. / Myllykoski, M. / Boeckers, T.M. / Kursula, P.
CitationJournal: J. Neurochem. / Year: 2018
Title: Structural basis for PDZ domain interactions in the post-synaptic density scaffolding protein Shank3.
Authors: Ponna, S.K. / Ruskamo, S. / Myllykoski, M. / Keller, C. / Boeckers, T.M. / Kursula, P.
History
DepositionAug 28, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 7, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 11, 2018Group: Data collection / Database references / Category: citation
Item: _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
A: SH3 and multiple ankyrin repeat domains protein 3
B: SH3 and multiple ankyrin repeat domains protein 3


Theoretical massNumber of molelcules
Total (without water)20,8002
Polymers20,8002
Non-polymers00
Water1086
1
A: SH3 and multiple ankyrin repeat domains protein 3


Theoretical massNumber of molelcules
Total (without water)10,4001
Polymers10,4001
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: SH3 and multiple ankyrin repeat domains protein 3


Theoretical massNumber of molelcules
Total (without water)10,4001
Polymers10,4001
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.080, 48.530, 78.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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: 10400.004 Da / Num. of mol.: 2
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / 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: 2.06 Å3/Da / Density % sol: 40.41 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M sodium acetate, 2.0 M ammonium sulphate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 3, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. obs: 8035 / % possible obs: 99.4 % / Redundancy: 6.3 % / Biso Wilson estimate: 59.3 Å2 / CC1/2: 1 / Rrim(I) all: 0.057 / Net I/σ(I): 22.1
Reflection shellResolution: 2.3→2.36 Å / Redundancy: 6.8 % / CC1/2: 0.912 / Rrim(I) all: 1.167 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→25.272 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 41.1
RfactorNum. reflection% reflection
Rfree0.2966 786 9.84 %
Rwork0.2794 --
obs0.2813 7984 98.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.3→25.272 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1403 0 0 6 1409
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041427
X-RAY DIFFRACTIONf_angle_d0.7071929
X-RAY DIFFRACTIONf_dihedral_angle_d22.421839
X-RAY DIFFRACTIONf_chiral_restr0.051225
X-RAY DIFFRACTIONf_plane_restr0.006247
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3001-2.44410.47561290.41521168X-RAY DIFFRACTION98
2.4441-2.63260.44141300.38721169X-RAY DIFFRACTION99
2.6326-2.89720.47411250.3681165X-RAY DIFFRACTION98
2.8972-3.31560.36831340.36031201X-RAY DIFFRACTION100
3.3156-4.17430.2711290.26771211X-RAY DIFFRACTION99
4.1743-25.27320.22891390.21851284X-RAY DIFFRACTION99

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