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- PDB-1tp3: PDZ3 domain of PSD-95 protein complexed with KKETPV peptide ligand -

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Basic information

Entry
Database: PDB / ID: 1tp3
TitlePDZ3 domain of PSD-95 protein complexed with KKETPV peptide ligand
Components
  • KKETPV peptide ligand
  • Presynaptic density protein 95
KeywordsPROTEIN BINDING / PDZ domain
Function / homology
Function and homology information


RHO GTPases activate CIT / positive regulation of AMPA glutamate receptor clustering / neuronal ion channel clustering / P2Y1 nucleotide receptor binding / Neurexins and neuroligins / beta-1 adrenergic receptor binding / neuroligin family protein binding / structural constituent of postsynaptic density / proximal dendrite / positive regulation of neuron projection arborization ...RHO GTPases activate CIT / positive regulation of AMPA glutamate receptor clustering / neuronal ion channel clustering / P2Y1 nucleotide receptor binding / Neurexins and neuroligins / beta-1 adrenergic receptor binding / neuroligin family protein binding / structural constituent of postsynaptic density / proximal dendrite / positive regulation of neuron projection arborization / regulation of grooming behavior / synaptic vesicle maturation / embryo development / receptor localization to synapse / cerebellar mossy fiber / cellular response to potassium ion / protein localization to synapse / vocalization behavior / LGI-ADAM interactions / Trafficking of AMPA receptors / dendritic branch / neuron spine / Activation of Ca-permeable Kainate Receptor / AMPA glutamate receptor clustering / dendritic spine morphogenesis / juxtaparanode region of axon / frizzled binding / negative regulation of receptor internalization / dendritic spine organization / neuron projection terminus / acetylcholine receptor binding / postsynaptic neurotransmitter receptor diffusion trapping / establishment or maintenance of epithelial cell apical/basal polarity / positive regulation of synapse assembly / Synaptic adhesion-like molecules / regulation of NMDA receptor activity / RAF/MAP kinase cascade / neurotransmitter receptor localization to postsynaptic specialization membrane / positive regulation of dendrite morphogenesis / cortical cytoskeleton / locomotory exploration behavior / regulation of neuronal synaptic plasticity / kinesin binding / positive regulation of excitatory postsynaptic potential / social behavior / AMPA glutamate receptor complex / neuromuscular process controlling balance / excitatory synapse / positive regulation of protein tyrosine kinase activity / D1 dopamine receptor binding / Unblocking of NMDA receptors, glutamate binding and activation / glutamate receptor binding / positive regulation of synaptic transmission / beta-2 adrenergic receptor binding / extrinsic component of cytoplasmic side of plasma membrane / dendrite cytoplasm / synaptic membrane / cell periphery / PDZ domain binding / postsynaptic density membrane / ionotropic glutamate receptor binding / regulation of long-term neuronal synaptic plasticity / establishment of protein localization / neuromuscular junction / cerebral cortex development / kinase binding / cell-cell adhesion / cell-cell junction / synaptic vesicle / cell junction / positive regulation of cytosolic calcium ion concentration / scaffold protein binding / postsynapse / protein-containing complex assembly / chemical synaptic transmission / basolateral plasma membrane / postsynaptic membrane / protein phosphatase binding / dendritic spine / postsynaptic density / neuron projection / signaling receptor binding / glutamatergic synapse / synapse / dendrite / protein-containing complex binding / protein kinase binding / endoplasmic reticulum / membrane / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Polyubiquitination (PEST) N-terminal domain of MAGUK / Disks large homologue 1, N-terminal PEST domain / Polyubiquitination (PEST) N-terminal domain of MAGUK / PDZ-associated domain of NMDA receptors / PDZ-associated domain of NMDA receptors / Disks large 1-like / Guanylate kinase, conserved site / Guanylate kinase-like signature. / Guanylate kinase-like domain profile. / Guanylate kinase-like domain ...Polyubiquitination (PEST) N-terminal domain of MAGUK / Disks large homologue 1, N-terminal PEST domain / Polyubiquitination (PEST) N-terminal domain of MAGUK / PDZ-associated domain of NMDA receptors / PDZ-associated domain of NMDA receptors / Disks large 1-like / Guanylate kinase, conserved site / Guanylate kinase-like signature. / Guanylate kinase-like domain profile. / Guanylate kinase-like domain / Guanylate kinase/L-type calcium channel beta subunit / Guanylate kinase / Guanylate kinase homologues. / PDZ domain / Pdz3 Domain / PDZ domain / SH3 domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Roll / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
Disks large homolog 4
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
synthetic (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 Å
AuthorsSaro, D. / Martin, P. / Vickrey, J.F. / Griffin, A. / Kovari, L.C. / Spaller, M.R.
CitationJournal: To be Published
Title: Structure of the third PDZ domain of PSD-95 protein complexed with KKETPV peptide ligand
Authors: Saro, D. / Martin, P. / Vickrey, J.F. / Griffin, A. / Kovari, L.C. / Spaller, M.R.
History
DepositionJun 15, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 20, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 1, 2015Group: Database references / Structure summary
Revision 1.4Oct 11, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.5Aug 23, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Presynaptic density protein 95
B: KKETPV peptide ligand


Theoretical massNumber of molelcules
Total (without water)13,4412
Polymers13,4412
Non-polymers00
Water1,18966
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)89.663, 89.663, 89.663
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number213
Space group name H-MP4132

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Components

#1: Protein Presynaptic density protein 95 / PSD-95 / Presynaptic protein SAP90 / Synapse-associated protein 90 / Discs / large homolog 4


Mass: 12738.067 Da / Num. of mol.: 1 / Fragment: PDZ 3; residues 302-402
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: DLG4, DLGH4, PSD95 / Plasmid: pET / Cell line (production host): gold DE3 / Production host: Escherichia coli (E. coli) / References: UniProt: P31016
#2: Protein/peptide KKETPV peptide ligand


Mass: 702.838 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: The KKETPV peptide ligand was chemically synthesized using solid phase peptide synthesis.
Source: (synth.) synthetic (others)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 66 / 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: 2.4 Å3/Da / Density % sol: 49 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.9
Details: 1.0 M sodium citrate, 0.1 M HEPES, pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 27, 2004
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.99→23.96 Å / Num. all: 8916 / Num. obs: 8916 / % possible obs: 99.7 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 11.58 % / Net I/σ(I): 6
Reflection shellResolution: 1.99→2.06 Å / % possible all: 99.1

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
XDSdata reduction
d*TREKdata scaling
XTALVIEWrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1BE9

1be9


Resolution: 1.99→19.57 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.902 / SU B: 5.793 / SU ML: 0.156 / Cross valid method: THROUGHOUT / σ(F): 1 / ESU R: 0.21 / ESU R Free: 0.201 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2961 423 4.7 %RANDOM
Rwork0.2247 ---
all0.2328 8486 --
obs0.22788 8486 99.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 25.567 Å2
Refinement stepCycle: LAST / Resolution: 1.99→19.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms908 0 0 66 974
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0380.021920
X-RAY DIFFRACTIONr_bond_other_d0.0030.02851
X-RAY DIFFRACTIONr_angle_refined_deg2.7211.9631239
X-RAY DIFFRACTIONr_angle_other_deg1.22331973
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.0295119
X-RAY DIFFRACTIONr_chiral_restr0.1750.2139
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.021051
X-RAY DIFFRACTIONr_gen_planes_other0.0080.02182
X-RAY DIFFRACTIONr_nbd_refined0.2390.2205
X-RAY DIFFRACTIONr_nbd_other0.280.21049
X-RAY DIFFRACTIONr_nbtor_other0.1070.2633
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.180.256
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3980.220
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3580.244
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2510.211
X-RAY DIFFRACTIONr_mcbond_it1.6181.5595
X-RAY DIFFRACTIONr_mcangle_it2.5992947
X-RAY DIFFRACTIONr_scbond_it4.1293325
X-RAY DIFFRACTIONr_scangle_it6.6824.5292
LS refinement shellResolution: 1.99→2.041 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.351 32
Rwork0.253 606
Refinement TLS params.Method: refined / Origin x: 49.2566 Å / Origin y: 74.6078 Å / Origin z: 32.7672 Å
111213212223313233
T0.007 Å2-0.0017 Å2-0.0008 Å2-0.0061 Å2-0.0038 Å2--0.0029 Å2
L0.1032 °2-0.1149 °20.0739 °2-0.2247 °20.0802 °2--0.262 °2
S-0.0118 Å °0.0004 Å °-0.0055 Å °0.0064 Å °0.0095 Å °0.0025 Å °0.0067 Å °0.0121 Å °0.0023 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA301 - 4155 - 119
2X-RAY DIFFRACTION1BB420 - 4251 - 6

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