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Basic information

Entry
Database: PDB / ID: 5izu
TitleA new binding site outside the canonical PDZ domain determines the specific interaction between Shank and SAPAP and their function
Components
  • SH3 and multiple ankyrin repeat domains protein 3
  • peptide from Disks large-associated protein 3
KeywordsPROTEIN BINDING / Shank / SAPAP / PDZ / extension / synapse / specific interaction
Function / homology
Function and homology information


response to interleukin-17 / Neurexins and neuroligins / regulation of AMPA glutamate receptor clustering / guanylate kinase-associated protein clustering / striatal medium spiny neuron differentiation / synaptic receptor adaptor activity / postsynaptic density assembly / regulation of postsynaptic neurotransmitter receptor activity / embryonic epithelial tube formation / modification of synaptic structure ...response to interleukin-17 / Neurexins and neuroligins / regulation of AMPA glutamate receptor clustering / guanylate kinase-associated protein clustering / striatal medium spiny neuron differentiation / synaptic receptor adaptor activity / postsynaptic density assembly / regulation of postsynaptic neurotransmitter receptor activity / embryonic epithelial tube formation / modification of synaptic structure / postsynaptic specialization / positive regulation of synapse structural plasticity / signaling / 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 / cholinergic synapse / NMDA glutamate receptor clustering / vocalization behavior / RET signaling / regulation of behavioral fear response / neuron spine / regulation of dendritic spine morphogenesis / AMPA glutamate receptor clustering / dendritic spine morphogenesis / neural precursor cell proliferation / brain morphogenesis / locomotion / regulation of long-term synaptic potentiation / long-term synaptic depression / exploration behavior / ciliary membrane / regulation of postsynapse organization / regulation of long-term synaptic depression / positive regulation of dendritic spine development / locomotory exploration behavior / associative learning / positive regulation of excitatory postsynaptic potential / social behavior / neuromuscular process controlling balance / excitatory synapse / 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 / PDZ domain binding / long-term synaptic potentiation / modulation of chemical synaptic transmission / neuromuscular junction / regulation of synaptic plasticity / memory / SH3 domain binding / MAPK cascade / amyloid-beta binding / actin binding / gene expression / scaffold protein binding / protein-containing complex assembly / dendritic spine / molecular adaptor activity / postsynaptic density / learning or memory / neuron projection / protein domain specific binding / neuronal cell body / glutamatergic synapse / synapse / protein-containing complex binding / zinc ion binding / identical protein binding / plasma membrane / cytoplasm
Similarity search - Function
Disks large-associated protein 3 / SAPAP family / Guanylate-kinase-associated protein (GKAP) protein / : / PDZ domain 6 / PDZ domain / Variant SH3 domain / SAM domain (Sterile alpha motif) / SAM domain profile. / Sterile alpha motif. ...Disks large-associated protein 3 / SAPAP family / Guanylate-kinase-associated protein (GKAP) protein / : / 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 / 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
Similarity search - Domain/homology
SH3 and multiple ankyrin repeat domains protein 3 / Disks large-associated protein 3
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.494 Å
AuthorsShang, Y. / Zeng, M. / Zhang, M.
Funding support Hong Kong, China, 5items
OrganizationGrant numberCountry
Research Grants Council663811 Hong Kong
Research Grants Council663812 Hong Kong
Research Grants CouncilT13-607/12R Hong Kong
Research Grants CouncilAoE-M09-12 Hong Kong
Ministry of Science and Technology of the People's Republic of China (Chinese Ministry of Science and Technology)2014CB910204 China
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2016
Title: A binding site outside the canonical PDZ domain determines the specific interaction between Shank and SAPAP and their function
Authors: Zeng, M. / Shang, Y. / Guo, T. / He, Q. / Yung, W.H. / Liu, K. / Zhang, M.
History
DepositionMar 26, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 18, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 1, 2016Group: Database references
Revision 1.2Jun 15, 2016Group: Database references
Revision 1.3Aug 24, 2016Group: Source and taxonomy
Revision 1.4Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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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: peptide from Disks large-associated protein 3
C: SH3 and multiple ankyrin repeat domains protein 3
D: peptide from Disks large-associated protein 3


Theoretical massNumber of molelcules
Total (without water)34,5714
Polymers34,5714
Non-polymers00
Water1,71195
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6320 Å2
ΔGint-29 kcal/mol
Surface area14210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.824, 72.824, 116.360
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number151
Space group name H-MP3112
Components on special symmetry positions
IDModelComponents
11B-1011-

HOH

21C-707-

HOH

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Components

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


Mass: 15565.557 Da / Num. of mol.: 2 / Fragment: UNP residues 533-665
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Shank3 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q4ACU6
#2: Protein/peptide peptide from Disks large-associated protein 3 / SAPAP3


Mass: 1719.910 Da / Num. of mol.: 2 / Fragment: UNP residues 963-977 / Source method: obtained synthetically / Details: C-terminal extended PBM of SAPAP / Source: (synth.) Mus musculus (house mouse) / References: UniProt: Q6PFD5
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 95 / 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: 2.58 Å3/Da / Density % sol: 52.26 %
Crystal growTemperature: 289 K / Method: evaporation / pH: 5.5 / Details: 0.1 M Bis-Tris, 3.0 M NaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9793 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Sep 29, 2012
RadiationMonochromator: Synchrotron / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.494→50 Å / Num. obs: 12561 / % possible obs: 99.9 % / Redundancy: 6.3 % / Net I/σ(I): 35.2

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Processing

Software
NameVersionClassification
PHENIX1.7.3_928refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1Q3O

1q3o


Resolution: 2.494→42.763 Å / SU ML: 0.45 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.39
RfactorNum. reflection% reflection
Rfree0.2506 610 4.87 %
Rwork0.1831 --
obs0.1863 12524 99.78 %
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Bsol: 47.663 Å2 / ksol: 0.342 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-5.0088 Å2-0 Å2-0 Å2
2--5.0088 Å20 Å2
3----10.0175 Å2
Refinement stepCycle: LAST / Resolution: 2.494→42.763 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2137 0 0 95 2232
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082175
X-RAY DIFFRACTIONf_angle_d1.012954
X-RAY DIFFRACTIONf_dihedral_angle_d14.432780
X-RAY DIFFRACTIONf_chiral_restr0.065346
X-RAY DIFFRACTIONf_plane_restr0.005381
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4941-2.74510.38621480.27942932X-RAY DIFFRACTION99
2.7451-3.14220.3561470.21882955X-RAY DIFFRACTION100
3.1422-3.95840.25091590.18372969X-RAY DIFFRACTION100
3.9584-42.76930.19471560.15343058X-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)
13.79061.6087-2.37921.8578-1.39372.7130.0202-0.3286-0.2449-0.3080.3630.8027-0.1008-1.4326-0.28780.43180.0017-0.11930.86920.03270.409518.1569-0.74284.6677
24.3664-0.4949-1.762.80131.71047.18770.1872-0.32750.23750.38350.0167-0.1187-0.26590.0441-0.18140.21220.0090.0520.2329-0.01380.213312.473731.522916.2662
31.9107-0.9282-0.67875.92455.74835.9255-0.09650.04810.25120.44520.3589-0.30260.70010.2246-0.27110.2693-0.04550.08580.5374-0.08180.348325.414730.58826.4821
47.72740.97234.25144.57150.41146.81090.0571-0.63760.2146-0.09050.2247-0.26540.7920.1634-0.2420.30720.02080.06890.46660.02480.273922.868225.6241-1.1713
54.4035-0.8056-0.16732.49140.54486.48620.1341-0.1567-0.17470.22120.34110.1437-0.2147-1.0001-0.40670.23120.05640.00790.49460.12780.2822.29473.983424.4866
60.5220.124-1.20950.2845-0.70873.40310.01780.4197-0.5078-0.12710.5374-0.0359-0.106-0.77310.40290.3547-0.1625-0.12191.3241-0.15420.37212.9681-1.571912.3671
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 542:564)
2X-RAY DIFFRACTION2chain 'A' and (resseq 565:665)
3X-RAY DIFFRACTION3chain 'B' and (resseq 963:977)
4X-RAY DIFFRACTION4chain 'C' and (resseq 542:564)
5X-RAY DIFFRACTION5chain 'C' and (resseq 565:665)
6X-RAY DIFFRACTION6chain 'D' and (resseq 963:977)

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