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- PDB-5ovp: PDZ domain from rat Shank3 bound to the C terminus of CIRL -

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Basic information

Entry
Database: PDB / ID: 5ovp
TitlePDZ domain from rat Shank3 bound to the C terminus of CIRL
Components
  • Adhesion G protein-coupled receptor L1
  • 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


latrotoxin receptor activity / 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 ...latrotoxin receptor activity / 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 / positive regulation of synapse assembly / 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 / toxic substance binding / postsynaptic density, intracellular component / glial cell proliferation / synapse assembly / cell adhesion molecule binding / 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 / G protein-coupled receptor activity / regulation of synaptic plasticity / SH3 domain binding / memory / long-term synaptic potentiation / adenylate cyclase-activating G protein-coupled receptor signaling pathway / MAPK cascade / presynaptic membrane / actin binding / growth cone / carbohydrate binding / scaffold protein binding / gene expression / dendritic spine / learning or memory / cell surface receptor signaling pathway / neuron projection / postsynaptic density / axon / synapse / protein-containing complex binding / glutamatergic synapse / zinc ion binding / identical protein binding / plasma membrane / cytoplasm
Similarity search - Function
Latrophilin-1 / GPCR, family 2, latrophilin, C-terminal / GPCR, family 2, latrophilin / Latrophilin Cytoplasmic C-terminal region / : / D-galactoside/L-rhamnose binding SUEL lectin domain superfamily / D-galactoside/L-rhamnose binding SUEL lectin domain / D-galactoside/L-rhamnose binding SUEL lectin domain / SUEL-type lectin domain profile. / GAIN domain, N-terminal ...Latrophilin-1 / GPCR, family 2, latrophilin, C-terminal / GPCR, family 2, latrophilin / Latrophilin Cytoplasmic C-terminal region / : / D-galactoside/L-rhamnose binding SUEL lectin domain superfamily / D-galactoside/L-rhamnose binding SUEL lectin domain / D-galactoside/L-rhamnose binding SUEL lectin domain / SUEL-type lectin domain profile. / GAIN domain, N-terminal / GPCR-Autoproteolysis INducing (GAIN) domain / Olfactomedin-like domain / Olfactomedin-like domain / Olfactomedin-like domain profile. / Olfactomedin-like domains / GAIN domain superfamily / GPCR proteolysis site, GPS, motif / PDZ domain 6 / GPS motif / GAIN-B domain profile. / G-protein-coupled receptor proteolytic site domain / PDZ domain / Variant SH3 domain / SAM domain (Sterile alpha motif) / GPCR, family 2, extracellular hormone receptor domain / G-protein coupled receptors family 2 profile 1. / Domain present in hormone receptors / Hormone receptor domain / GPCR family 2, extracellular hormone receptor domain superfamily / G-protein coupled receptors family 2 signature 2. / GPCR, family 2, secretin-like, conserved site / GPCR, family 2, secretin-like / 7 transmembrane receptor (Secretin family) / GPCR, family 2-like / G-protein coupled receptors family 2 profile 2. / 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
Adhesion G protein-coupled receptor L1 / SH3 and multiple ankyrin repeat domains protein 3
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.5 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
Revision 1.2Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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: Adhesion G protein-coupled receptor L1


Theoretical massNumber of molelcules
Total (without water)11,0862
Polymers11,0862
Non-polymers00
Water1,13563
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1140 Å2
ΔGint-5 kcal/mol
Surface area5630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)32.090, 32.090, 150.220
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number153
Space group name H-MP3212
Components on special symmetry positions
IDModelComponents
11A-749-

HOH

21A-751-

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 / Fragment: PDZ domain, UNP residues 570-664
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 Adhesion G protein-coupled receptor L1 / Calcium-independent alpha-latrotoxin receptor 1 / CIRL-1 / Latrophilin-1


Mass: 685.810 Da / Num. of mol.: 1 / Fragment: UNP residues 1510-1515 / Source method: obtained synthetically / Source: (synth.) Rattus norvegicus (Norway rat) / References: UniProt: O88917
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 63 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.01 Å3/Da / Density % sol: 38.93 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M HEPES pH 7.5, 2% PEG 400, 2 M ammonium sulphate

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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 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 28, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 14688 / % possible obs: 99.7 % / Redundancy: 10.7 % / Biso Wilson estimate: 28 Å2 / CC1/2: 1 / Rrim(I) all: 0.095 / Net I/σ(I): 15.4
Reflection shellResolution: 1.5→1.54 Å / Redundancy: 10 % / Num. unique obs: 1055 / CC1/2: 0.557 / Rrim(I) all: 2.457 / % possible all: 98.4

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementResolution: 1.5→27.791 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 30.91
RfactorNum. reflection% reflection
Rfree0.2355 737 5.04 %
Rwork0.1934 --
obs0.1954 14613 99.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.5→27.791 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms783 0 0 63 846
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011813
X-RAY DIFFRACTIONf_angle_d1.0381104
X-RAY DIFFRACTIONf_dihedral_angle_d21.263299
X-RAY DIFFRACTIONf_chiral_restr0.085131
X-RAY DIFFRACTIONf_plane_restr0.008143
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.61580.37631440.33652728X-RAY DIFFRACTION99
1.6158-1.77840.27821490.26482733X-RAY DIFFRACTION100
1.7784-2.03560.24711460.20112739X-RAY DIFFRACTION100
2.0356-2.56440.23191470.1922781X-RAY DIFFRACTION100
2.5644-27.79550.2151510.17022895X-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)
11.1456-0.6894-0.20630.542-0.15971.571-0.0885-0.08930.07240.11390.1514-0.00470.14840.17630.00080.17540.0067-0.0070.1746-0.0190.1726-8.3068-6.015514.1081
20.0338-0.1690.0072-0.0087-0.05340.00710.1952-0.0323-0.0677-0.0011-0.086-0.0698-0.30880.20080.00010.2160.03760.00430.27550.01880.2192-5.9267-6.263619.0146
30.06740.0565-0.03070.0516-0.05750.05490.16890.00950.1603-0.15430.0427-0.3616-0.1299-0.1483-0.00010.23440.015-0.01380.2057-0.00650.1642-12.292-5.2765.003
41.0680.1225-0.18880.3514-0.81951.12550.0533-0.07230.0883-0.07570.1969-0.0764-0.066-0.14970.14260.22420.0668-0.0280.1710.00710.1471-11.3504-6.8613.3467
50.4824-0.0264-0.73350.45490.00581.1226-0.31470.3004-0.2938-0.56870.3565-0.25590.30410.0896-0.00590.27440.19340.10670.1908-0.05560.27940.423-17.05869.3722
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 617 through 662 )
2X-RAY DIFFRACTION2chain 'A' and (resid 663 through 674 )
3X-RAY DIFFRACTION3chain 'B' and (resid 1510 through 1515 )
4X-RAY DIFFRACTION4chain 'A' and (resid 579 through 607 )
5X-RAY DIFFRACTION5chain 'A' and (resid 608 through 616 )

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