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- PDB-1q3p: Crystal structure of the Shank PDZ-ligand complex reveals a class... -

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Basic information

Entry
Database: PDB / ID: 1q3p
TitleCrystal structure of the Shank PDZ-ligand complex reveals a class I PDZ interaction and a novel PDZ-PDZ dimerization
Components
  • C-terminal hexapeptide from Guanylate kinase-associated protein
  • Shank1
KeywordsPEPTIDE BINDING PROTEIN / shank / PDZ / GKAP
Function / homology
Function and homology information


somatostatin receptor binding / determination of affect / synaptic receptor adaptor activity / olfactory behavior / synapse maturation / Neurexins and neuroligins / negative regulation of actin filament bundle assembly / structural constituent of postsynaptic density / righting reflex / protein localization to synapse ...somatostatin receptor binding / determination of affect / synaptic receptor adaptor activity / olfactory behavior / synapse maturation / Neurexins and neuroligins / negative regulation of actin filament bundle assembly / structural constituent of postsynaptic density / righting reflex / protein localization to synapse / vocalization behavior / habituation / regulation of AMPA receptor activity / ankyrin repeat binding / dendritic spine morphogenesis / adult behavior / positive regulation of dendritic spine development / social behavior / associative learning / positive regulation of excitatory postsynaptic potential / neuromuscular process controlling balance / excitatory synapse / long-term memory / ionotropic glutamate receptor binding / G protein-coupled receptor binding / modulation of chemical synaptic transmission / Schaffer collateral - CA1 synapse / SH3 domain binding / signaling receptor complex adaptor activity / scaffold protein binding / postsynaptic membrane / protein-containing complex assembly / dendritic spine / postsynaptic density / neuron projection / dendrite / synapse / glutamatergic synapse / protein-containing complex binding / membrane / identical protein binding / plasma membrane / cytosol
Similarity search - Function
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 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
: / SH3 and multiple ankyrin repeat domains protein 1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsIm, Y.J. / Lee, J.H. / Park, S.H. / Park, S.J. / Rho, S.-H. / Kang, G.B. / Kim, E. / Eom, S.H.
CitationJournal: J.Biol.Chem. / Year: 2003
Title: Crystal structure of the Shank PDZ-ligand complex reveals a class I PDZ interaction and a novel PDZ-PDZ dimerization
Authors: Im, Y.J. / Lee, J.H. / Park, S.H. / Park, S.J. / Rho, S.-H. / Kang, G.B. / Kim, E. / Eom, S.H.
History
DepositionJul 31, 2003Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 27, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 2023Group: 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: Shank1
B: Shank1
C: C-terminal hexapeptide from Guanylate kinase-associated protein
D: C-terminal hexapeptide from Guanylate kinase-associated protein


Theoretical massNumber of molelcules
Total (without water)25,5844
Polymers25,5844
Non-polymers00
Water79344
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3190 Å2
ΔGint-7 kcal/mol
Surface area11420 Å2
MethodPISA
2
A: Shank1
B: Shank1
C: C-terminal hexapeptide from Guanylate kinase-associated protein
D: C-terminal hexapeptide from Guanylate kinase-associated protein

A: Shank1
B: Shank1
C: C-terminal hexapeptide from Guanylate kinase-associated protein
D: C-terminal hexapeptide from Guanylate kinase-associated protein


Theoretical massNumber of molelcules
Total (without water)51,1678
Polymers51,1678
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area8500 Å2
ΔGint-23 kcal/mol
Surface area20740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.763, 60.763, 157.902
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Shank1 /


Mass: 12073.959 Da / Num. of mol.: 2 / Fragment: PDZ domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: shank1 / Plasmid: pGEX4T1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9WV48
#2: Protein/peptide C-terminal hexapeptide from Guanylate kinase-associated protein / C-terminal hexapeptide from GKAP


Mass: 717.791 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: EAQTRL sequence is the C-terminal hexapeptide of GKAP protein in rattus norvegicus
References: GenBank: 19923689
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 44 / 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: 3.04 Å3/Da / Density % sol: 59.25 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG 6000, KCl, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Crystal grow
*PLUS
pH: 7.4 / Method: vapor diffusion, hanging drop / Details: Park, S.H., (2002) Acta Cryst., D58, 1353.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
112 mg/mlprotein1drop
250 mMTris-HCl1droppH7.4
32 mMpeptide1drop
416 %(w/v)PEG60001reservoir
50.2 M1reservoirKCl
6100 mMMES-NaOH1reservoirpH6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 6B / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 26, 2002 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.25→30 Å / Num. all: 64296 / Num. obs: 61853 / % possible obs: 96.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 4 / Redundancy: 4.3 % / Biso Wilson estimate: 30.3 Å2 / Rmerge(I) obs: 0.041 / Rsym value: 0.041 / Net I/σ(I): 50.9
Reflection shellResolution: 2.25→2.29 Å / Rmerge(I) obs: 0.258 / Mean I/σ(I) obs: 6.6 / Rsym value: 0.258 / % possible all: 96.5
Reflection shell
*PLUS
% possible obs: 95.6 %

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1Q3O

1q3o


Resolution: 2.25→29.84 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 840523.46 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.28 718 5 %RANDOM
Rwork0.251 ---
all0.253 14786 --
obs0.251 14239 96.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 52.5189 Å2 / ksol: 0.359095 e/Å3
Displacement parametersBiso mean: 44.1 Å2
Baniso -1Baniso -2Baniso -3
1-0.78 Å20 Å20 Å2
2--0.78 Å20 Å2
3----1.57 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.38 Å0.34 Å
Luzzati d res low-5 Å
Luzzati sigma a0.3 Å0.3 Å
Refinement stepCycle: LAST / Resolution: 2.25→29.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1667 0 0 44 1711
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.7
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.651.5
X-RAY DIFFRACTIONc_mcangle_it2.782
X-RAY DIFFRACTIONc_scbond_it2.222
X-RAY DIFFRACTIONc_scangle_it3.342.5
LS refinement shellResolution: 2.25→2.39 Å / Rfactor Rfree error: 0.028 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.312 126 5.5 %
Rwork0.293 2183 -
obs--96.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
Refinement
*PLUS
Lowest resolution: 30 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.28
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg25.4
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.7

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