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- PDB-5ovc: PDZ domain from rat Shank3 bound to the C terminus of GKAP -

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Basic information

Entry
Database: PDB / ID: 5ovc
TitlePDZ domain from rat Shank3 bound to the C terminus of GKAP
Components
  • GKAP C terminus, synthetic peptide
  • 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


response to interleukin-17 / regulation of AMPA glutamate receptor clustering / guanylate kinase-associated protein clustering / striatal medium spiny neuron differentiation / synaptic receptor adaptor activity / maintenance of postsynaptic density structure / RET signaling / positive regulation of glutamate receptor signaling pathway / postsynaptic density assembly / embryonic epithelial tube formation ...response to interleukin-17 / regulation of AMPA glutamate receptor clustering / guanylate kinase-associated protein clustering / striatal medium spiny neuron differentiation / synaptic receptor adaptor activity / maintenance of postsynaptic density structure / RET signaling / positive regulation of glutamate receptor signaling pathway / postsynaptic density assembly / embryonic epithelial tube formation / postsynaptic specialization / Neurexins and neuroligins / positive regulation of synapse structural plasticity / signaling / negative regulation of actin filament bundle assembly / vocal learning / negative regulation of cell volume / positive regulation of long-term neuronal synaptic plasticity / structural constituent of postsynaptic density / regulation of grooming behavior / protein localization to synapse / NMDA glutamate receptor clustering / vocalization behavior / regulation of dendritic spine morphogenesis / regulation of behavioral fear response / neuron spine / AMPA glutamate receptor clustering / neural precursor cell proliferation / locomotion / dendritic spine morphogenesis / brain morphogenesis / aggresome assembly / regulation of long-term synaptic potentiation / positive regulation of AMPA receptor activity / long-term synaptic depression / regulation of postsynapse organization / ciliary membrane / exploration behavior / regulation of long-term synaptic depression / adult behavior / positive regulation of dendritic spine development / locomotory exploration behavior / postsynaptic density, intracellular component / social behavior / associative learning / positive regulation of excitatory postsynaptic potential / neuromuscular process controlling balance / glial cell proliferation / regulation of proteasomal protein catabolic process / synapse assembly / ionotropic glutamate receptor binding / positive regulation of synaptic transmission, glutamatergic / locomotory behavior / learning / long-term synaptic potentiation / positive regulation of long-term synaptic potentiation / G protein-coupled receptor binding / regulation of synaptic plasticity / modulation of chemical synaptic transmission / memory / SH3 domain binding / : / MAPK cascade / gene expression / actin binding / scaffold protein binding / postsynaptic membrane / dendritic spine / postsynaptic density / learning or memory / molecular adaptor activity / neuron projection / protein domain specific binding / synapse / glutamatergic synapse / protein-containing complex binding / zinc ion binding / identical protein binding / plasma membrane / cytoplasm
Similarity search - Function
SAPAP family / Guanylate-kinase-associated protein (GKAP) protein / PDZ domain 6 / PDZ domain / Variant SH3 domain / SAM domain (Sterile alpha motif) / PDZ domain / Pdz3 Domain / SAM domain profile. / Sterile alpha motif. ...SAPAP family / Guanylate-kinase-associated protein (GKAP) protein / 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 / Ankyrin repeats (3 copies) / PDZ superfamily / 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
Disks large-associated protein 1 / SH3 and multiple ankyrin repeat domains protein 3
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SH3 and multiple ankyrin repeat domains protein 3
B: GKAP C terminus, synthetic peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,1793
Polymers11,1442
Non-polymers351
Water2,360131
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1420 Å2
ΔGint-17 kcal/mol
Surface area5680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.550, 51.550, 81.770
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-875-

HOH

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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.: 1
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: Protein/peptide GKAP C terminus, synthetic peptide


Mass: 743.829 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Rattus norvegicus (Norway rat) / References: UniProt: P97836*PLUS
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 131 / 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: 2.44 Å3/Da / Density % sol: 49.54 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 1.6M sodium citrate pH 6.5

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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: May 3, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.55→50 Å / Num. obs: 30593 / % possible obs: 99.9 % / Redundancy: 6.7 % / CC1/2: 0.999 / Rrim(I) all: 0.126 / Net I/σ(I): 22.1
Reflection shellResolution: 1.55→1.59 Å / Redundancy: 6 % / Num. unique obs: 2244 / CC1/2: 0.132 / Rrim(I) all: 3.628 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.55→43.608 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.32 / Phase error: 24.01
RfactorNum. reflection% reflection
Rfree0.2071 1540 5.04 %
Rwork0.1754 --
obs0.177 30539 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.55→43.608 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms787 0 1 131 919
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004842
X-RAY DIFFRACTIONf_angle_d0.6171144
X-RAY DIFFRACTIONf_dihedral_angle_d19.39505
X-RAY DIFFRACTIONf_chiral_restr0.048130
X-RAY DIFFRACTIONf_plane_restr0.005152
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.55-1.60.43411410.36982614X-RAY DIFFRACTION100
1.6-1.65720.32091470.3312655X-RAY DIFFRACTION100
1.6572-1.72360.23741430.29322632X-RAY DIFFRACTION100
1.7236-1.8020.26881350.25072625X-RAY DIFFRACTION100
1.802-1.8970.31631350.2342649X-RAY DIFFRACTION100
1.897-2.01590.29621340.2142635X-RAY DIFFRACTION100
2.0159-2.17150.19771360.16762632X-RAY DIFFRACTION100
2.1715-2.39010.20771400.17322640X-RAY DIFFRACTION100
2.3901-2.73590.21691410.1522644X-RAY DIFFRACTION100
2.7359-3.44670.15031440.15542652X-RAY DIFFRACTION100
3.4467-43.62490.17881440.14072621X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.68170.688-0.97391.5346-1.04152.47570.0543-0.2336-0.0651-0.0164-0.1784-0.09560.08890.27270.11880.20090.0007-0.02610.20660.02780.211912.0621-13.8705-10.0619
23.09810.2560.92991.6556-0.10882.83290.1004-0.01790.0576-0.0536-0.11910.09610.1938-0.31920.01120.2234-0.0084-0.01310.2101-0.02360.1778-3.5607-16.1154-18.7991
30.82250.19280.81381.93750.89162.923-0.0099-0.1954-0.16070.2221-0.08140.10190.1338-0.47940.12470.1949-0.00290.00320.2747-0.02860.1998-6.7029-13.9424-10.7804
45.2730.89752.47612.21020.73525.8758-0.1215-0.26280.6343-0.0487-0.209-0.0105-0.4351-0.17880.36120.22270.0189-0.02570.2026-0.03880.254-0.2086-5.4816-12.0686
57.27684.42362.22695.64930.86953.4181-0.071-0.0517-0.25-0.2872-0.02320.01770.2058-0.1128-0.02270.25960.0201-0.01420.16980.00590.20820.8754-17.9346-10.2633
65.7836-0.30540.83170.74270.06620.1571-0.2420.04250.0382-0.16750.0812-0.0084-0.0666-0.05760.21790.24160.0134-0.01520.22290.01780.19511.673-9.9616-22.4093
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 579 through 592 )
2X-RAY DIFFRACTION2chain 'A' and (resid 593 through 636 )
3X-RAY DIFFRACTION3chain 'A' and (resid 637 through 651 )
4X-RAY DIFFRACTION4chain 'A' and (resid 652 through 662 )
5X-RAY DIFFRACTION5chain 'A' and (resid 663 through 674 )
6X-RAY DIFFRACTION6chain 'B' and (resid 987 through 992 )

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