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- PDB-6exj: PDZ domain from rat Shank3 bound to the C terminus of somatostati... -

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Basic information

Entry
Database: PDB / ID: 6exj
TitlePDZ domain from rat Shank3 bound to the C terminus of somatostatin receptor subtype 2
Components
  • SH3 and multiple ankyrin repeat domains protein 3
  • SSTR2
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 / postsynaptic density assembly / Peptide ligand-binding receptors / somatostatin 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 / maintenance of postsynaptic density structure / RET signaling / postsynaptic density assembly / Peptide ligand-binding receptors / somatostatin receptor activity / embryonic epithelial tube formation / Neurexins and neuroligins / positive regulation of synapse structural plasticity / vocal learning / negative regulation of actin filament bundle assembly / negative regulation of cell volume / structural constituent of postsynaptic density / positive regulation of glutamate receptor signaling pathway / regulation of grooming behavior / positive regulation of long-term neuronal synaptic plasticity / peristalsis / regulation of muscle contraction / NMDA glutamate receptor clustering / vocalization behavior / regulation of behavioral fear response / neuron spine / regulation of dendritic spine morphogenesis / AMPA glutamate receptor clustering / neuropeptide binding / dendritic spine morphogenesis / neural precursor cell proliferation / brain morphogenesis / locomotion / G alpha (i) signalling events / cellular response to glucocorticoid stimulus / regulation of long-term synaptic potentiation / positive regulation of AMPA receptor activity / long-term synaptic depression / ciliary membrane / exploration behavior / regulation of postsynapse organization / regulation of long-term synaptic depression / adult behavior / positive regulation of dendritic spine development / locomotory exploration behavior / plasma membrane => GO:0005886 / response to starvation / associative learning / positive regulation of excitatory postsynaptic potential / social behavior / neuromuscular process controlling balance / neuropeptide signaling pathway / postsynaptic density, intracellular component / glial cell proliferation / forebrain development / synapse assembly / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / positive regulation of synaptic transmission, glutamatergic / cerebellum development / learning / positive regulation of long-term synaptic potentiation / locomotory behavior / cellular response to estradiol stimulus / PDZ domain binding / G protein-coupled receptor binding / G protein-coupled receptor activity / long-term synaptic potentiation / peptide binding / ionotropic glutamate receptor binding / modulation of chemical synaptic transmission / regulation of synaptic plasticity / memory / SH3 domain binding / : / MAPK cascade / actin binding / gene expression / scaffold protein binding / spermatogenesis / postsynaptic membrane / dendritic spine / postsynaptic density / learning or memory / neuron projection / G protein-coupled receptor signaling pathway / glutamatergic synapse / protein-containing complex binding / zinc ion binding / identical protein binding / membrane / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Somatostatin receptor 2 / Somatostatin receptor family / PDZ domain 6 / PDZ domain / Variant SH3 domain / SAM domain (Sterile alpha motif) / PDZ domain / Pdz3 Domain / SAM domain profile. / Sterile alpha motif. ...Somatostatin receptor 2 / Somatostatin receptor family / 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 / Serpentine type 7TM GPCR chemoreceptor Srsx / 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 / G-protein coupled receptors family 1 signature. / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile. / 7 transmembrane receptor (rhodopsin family) / Roll / Mainly Beta
Similarity search - Domain/homology
Somatostatin receptor type 2 / SH3 and multiple ankyrin repeat domains protein 3
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsPonna, S.K. / Keller, C. / Ruskamo, S. / 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
DepositionNov 8, 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 1.2Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: SSTR2
C: SH3 and multiple ankyrin repeat domains protein 3
D: SSTR2


Theoretical massNumber of molelcules
Total (without water)22,2044
Polymers22,2044
Non-polymers00
Water61334
1
A: SH3 and multiple ankyrin repeat domains protein 3
B: SSTR2


Theoretical massNumber of molelcules
Total (without water)11,1022
Polymers11,1022
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1220 Å2
ΔGint-5 kcal/mol
Surface area5670 Å2
MethodPISA
2
C: SH3 and multiple ankyrin repeat domains protein 3
D: SSTR2


Theoretical massNumber of molelcules
Total (without water)11,1022
Polymers11,1022
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1210 Å2
ΔGint-5 kcal/mol
Surface area5570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.850, 43.300, 78.760
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: Protein/peptide SSTR2


Mass: 701.767 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Rattus norvegicus (Norway rat) / References: UniProt: P30680*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 34 / 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

Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 2 M ammonium sulphate, 0.2 M NaCl, 0.1 M MES

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.976 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 27, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 14124 / % possible obs: 99.9 % / Redundancy: 6.2 % / Biso Wilson estimate: 42.7 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.071 / Net I/σ(I): 13.8
Reflection shellResolution: 1.8→1.85 Å / Redundancy: 6.3 % / Mean I/σ(I) obs: 0.7 / Num. unique obs: 1020 / CC1/2: 0.54 / Rrim(I) all: 2.515 / % possible all: 99.6

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5OVC

5ovc


Resolution: 1.8→37.944 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 35.01
RfactorNum. reflection% reflection
Rfree0.2739 1416 10.06 %
Rwork0.2249 --
obs0.2296 14079 99.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.8→37.944 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1452 0 0 34 1486
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.021469
X-RAY DIFFRACTIONf_angle_d1.6011981
X-RAY DIFFRACTIONf_dihedral_angle_d21.79870
X-RAY DIFFRACTIONf_chiral_restr0.078235
X-RAY DIFFRACTIONf_plane_restr0.012254
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8002-1.86460.39171380.4031229X-RAY DIFFRACTION99
1.8646-1.93920.45271370.34371241X-RAY DIFFRACTION99
1.9392-2.02750.31641410.31081234X-RAY DIFFRACTION99
2.0275-2.13430.3971410.30241253X-RAY DIFFRACTION100
2.1343-2.2680.37581400.27611254X-RAY DIFFRACTION100
2.268-2.44310.27961400.25221246X-RAY DIFFRACTION100
2.4431-2.68890.30661450.26251270X-RAY DIFFRACTION100
2.6889-3.07790.22941410.24061275X-RAY DIFFRACTION100
3.0779-3.87720.27111460.19011291X-RAY DIFFRACTION100
3.8772-37.95220.23241470.18891370X-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)
13.57971.6986-0.15123.8866-1.95143.01250.2259-0.61681.13540.6466-0.03730.6092-0.1253-0.0717-0.1590.3953-0.07380.04730.5444-0.16990.44651.573896.170420.7037
22.74153.70141.66695.41742.01216.96580.89361.0947-0.6314-0.6397-1.0117-0.3606-0.04270.7468-0.1950.45030.1829-0.00260.81630.01960.415323.232695.636215.4303
38.54972.068-1.48413.87822.05995.03630.5355-0.13351.1215-0.4379-0.57230.6906-0.9524-0.4154-0.05030.5378-0.00780.00570.4085-0.05760.594.5705101.552314.6974
43.7165-2.3979-0.27065.9061.53048.05440.1789-0.88650.54880.9941-0.26470.05350.21580.6565-0.03560.5249-0.1542-0.03810.558-0.00850.384915.688197.303824.0298
52.2032-2.2481-3.74196.3797-1.18979.162-0.1849-0.7126-1.48191.3001-0.27610.54611.6556-0.83340.58410.6953-0.1343-0.00540.48880.07190.449210.647488.236822.7627
68.063.51040.58257.77910.70820.5670.5492-0.18960.30010.419-0.16530.47640.37-0.3502-0.20350.5159-0.15980.00170.7552-0.10590.44198.2055100.487723.0827
76.6469-0.68250.63269.5614-0.1298.3389-0.6616-0.6587-0.21710.18020.0903-0.10091.3295-0.37420.50540.55840.0064-0.01930.5305-0.04250.30279.735589.989512.8685
85.40892.9214-2.21294.01971.41112.5024-0.46220.51171.0608-1.62160.39081.2817-0.1852-0.0835-0.02730.6827-0.1089-0.26820.35530.03490.50810.983895.8317-0.8466
97.58822.02231.6435.59221.05267.8297-0.18540.03280.5870.23110.1640.20190.35110.08960.1950.2571-0.0334-0.0010.35730.05120.2815-0.57685.45194.9274
108.7135-0.4229-0.91924.42630.06278.9083-0.27380.79950.2848-0.69890.28080.58820.2669-0.3890.03680.4476-0.1103-0.0370.40860.03270.3799-2.016484.1304-2.0568
115.19491.4839-1.20385.64563.82983.6899-0.51840.96370.4101-2.20370.6273-0.317-1.06762.04670.19490.7324-0.28590.06190.731-0.00780.40798.226488.7564-3.8611
128.20611.6029-0.84139.1927-1.72432.1203-0.52950.4068-0.2019-0.4749-1.00140.9241-2.09810.76260.08920.7775-0.2547-0.22990.44850.10170.2773-5.203487.3867-2.5317
138.4129-3.09520.44418.29240.61375.67640.13360.5052-0.36080.0308-0.67130.78610.05291.01510.35530.5430.0516-0.05370.4677-0.01420.36577.350187.64266.7874
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 644 through 662 )
2X-RAY DIFFRACTION2chain 'A' and (resid 663 through 681 )
3X-RAY DIFFRACTION3chain 'A' and (resid 682 through 701 )
4X-RAY DIFFRACTION4chain 'A' and (resid 702 through 716 )
5X-RAY DIFFRACTION5chain 'A' and (resid 717 through 726 )
6X-RAY DIFFRACTION6chain 'A' and (resid 727 through 739 )
7X-RAY DIFFRACTION7chain 'B' and (resid 364 through 369 )
8X-RAY DIFFRACTION8chain 'C' and (resid 644 through 662 )
9X-RAY DIFFRACTION9chain 'C' and (resid 663 through 695 )
10X-RAY DIFFRACTION10chain 'C' and (resid 696 through 716 )
11X-RAY DIFFRACTION11chain 'C' and (resid 717 through 729 )
12X-RAY DIFFRACTION12chain 'C' and (resid 730 through 739 )
13X-RAY DIFFRACTION13chain 'D' and (resid 364 through 369 )

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