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- PDB-5ovv: PDZ domain from rat Shank3 bound to the C terminus of ProSAPiP1 -

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Basic information

Entry
Database: PDB / ID: 5ovv
TitlePDZ domain from rat Shank3 bound to the C terminus of ProSAPiP1
Components
  • Leucine zipper putative tumor suppressor 3
  • SH3 and multiple ankyrin repeat domains protein 3
KeywordsPROTEIN BINDING / PDZ domain / peptide binding / post-synaptic density / C terminus
Function / homology
Function and homology information


plasma membrane bounded cell projection / 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 ...plasma membrane bounded cell projection / 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 / regulation of postsynapse assembly / 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 long-term neuronal synaptic plasticity / positive regulation of glutamate receptor signaling pathway / regulation of grooming behavior / negative regulation of cell volume / 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 / ionotropic glutamate receptor binding / synapse assembly / positive regulation of synaptic transmission, glutamatergic / learning / positive regulation of long-term synaptic potentiation / long-term synaptic potentiation / locomotory behavior / G protein-coupled receptor binding / PDZ domain binding / synapse organization / modulation of chemical synaptic transmission / protein homooligomerization / regulation of synaptic plasticity / memory / SH3 domain binding / MAPK cascade / actin binding / gene expression / scaffold protein binding / dendritic spine / postsynaptic density / learning or memory / cytoskeleton / neuron projection / glutamatergic synapse / synapse / protein-containing complex binding / zinc ion binding / identical protein binding / plasma membrane / cytoplasm
Similarity search - Function
Leucine zipper putative tumor suppressor / Fez1 / : / PDZ domain 6 / PDZ domain / Variant SH3 domain / SAM domain (Sterile alpha motif) / SAM domain profile. / Sterile alpha motif. / Sterile alpha motif domain ...Leucine zipper putative tumor suppressor / Fez1 / : / PDZ domain 6 / PDZ domain / Variant SH3 domain / SAM domain (Sterile alpha motif) / 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
Similarity search - Domain/homology
THIOCYANATE ION / SH3 and multiple ankyrin repeat domains 3 / Leucine zipper putative tumor suppressor 3 / SH3 and multiple ankyrin repeat domains protein 3
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.4 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 29, 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

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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: Leucine zipper putative tumor suppressor 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,4094
Polymers14,2932
Non-polymers1162
Water2,504139
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1270 Å2
ΔGint-7 kcal/mol
Surface area6270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.570, 85.910, 46.060
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein SH3 and multiple ankyrin repeat domains protein 3


Mass: 13576.530 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Shank3 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0U1RRP5, UniProt: Q9JLU4*PLUS
#2: Protein/peptide Leucine zipper putative tumor suppressor 3 / ProSAP-interacting protein 1 / ProSAPiP1


Mass: 716.778 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Rattus norvegicus (Norway rat) / References: UniProt: Q8K1Q4
#3: Chemical ChemComp-SCN / THIOCYANATE ION


Mass: 58.082 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CNS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 139 / 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: 2.53 Å3/Da / Density % sol: 51.37 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: Sodium thiocyanate 200 mM, 23% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 1, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.4→50 Å / Num. obs: 22464 / % possible obs: 99.8 % / Redundancy: 12.6 % / Biso Wilson estimate: 20 Å2 / CC1/2: 0.996 / Rrim(I) all: 0.218 / Net I/σ(I): 8.2
Reflection shellResolution: 1.4→1.44 Å / Redundancy: 11.5 % / Num. unique obs: 1644 / CC1/2: 0.333 / Rrim(I) all: 2.177 / % possible all: 99.2

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementResolution: 1.4→42.955 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.1 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1968 1122 5 %
Rwork0.1551 --
obs0.1573 22447 99.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.4→42.955 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms817 0 6 139 962
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01893
X-RAY DIFFRACTIONf_angle_d1.0961212
X-RAY DIFFRACTIONf_dihedral_angle_d23.222327
X-RAY DIFFRACTIONf_chiral_restr0.079138
X-RAY DIFFRACTIONf_plane_restr0.007160
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4003-1.4640.27991380.25012628X-RAY DIFFRACTION99
1.464-1.54120.28211380.23562605X-RAY DIFFRACTION100
1.5412-1.63780.30511380.19172632X-RAY DIFFRACTION100
1.6378-1.76430.26411390.16382649X-RAY DIFFRACTION100
1.7643-1.94180.1731390.13122649X-RAY DIFFRACTION100
1.9418-2.22280.17591410.1162662X-RAY DIFFRACTION100
2.2228-2.80040.17991410.14042686X-RAY DIFFRACTION100
2.8004-42.97520.17241480.15722814X-RAY DIFFRACTION100

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