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- PDB-1tq3: Higher resolution crystal structure of the third PDZ domain of po... -

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Basic information

Entry
Database: PDB / ID: 1tq3
TitleHigher resolution crystal structure of the third PDZ domain of post synaptic PSD-95 protein
ComponentsPresynaptic density protein 95
KeywordsPEPTIDE BINDING PROTEIN
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 / synaptic vesicle maturation / 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 / synaptic vesicle maturation / positive regulation of neuron projection arborization / regulation of grooming behavior / receptor localization to synapse / protein localization to synapse / vocalization behavior / cerebellar mossy fiber / proximal dendrite / LGI-ADAM interactions / cellular response to potassium ion / Trafficking of AMPA receptors / neuron spine / Activation of Ca-permeable Kainate Receptor / AMPA glutamate receptor clustering / dendritic branch / dendritic spine morphogenesis / establishment or maintenance of epithelial cell apical/basal polarity / frizzled binding / juxtaparanode region of axon / dendritic spine organization / negative regulation of receptor internalization / neuron projection terminus / postsynaptic neurotransmitter receptor diffusion trapping / acetylcholine receptor binding / positive regulation of synapse assembly / regulation of NMDA receptor activity / Synaptic adhesion-like molecules / positive regulation of dendrite morphogenesis / RAF/MAP kinase cascade / beta-2 adrenergic receptor binding / neurotransmitter receptor localization to postsynaptic specialization membrane / cortical cytoskeleton / locomotory exploration behavior / extrinsic component of cytoplasmic side of plasma membrane / regulation of neuronal synaptic plasticity / kinesin binding / AMPA glutamate receptor complex / social behavior / neuromuscular process controlling balance / positive regulation of protein tyrosine kinase activity / positive regulation of excitatory postsynaptic potential / excitatory synapse / D1 dopamine receptor binding / Unblocking of NMDA receptors, glutamate binding and activation / positive regulation of synaptic transmission / glutamate receptor binding / ionotropic glutamate receptor binding / dendrite cytoplasm / cell periphery / synaptic membrane / PDZ domain binding / postsynaptic density membrane / regulation of long-term neuronal synaptic plasticity / establishment of protein localization / neuromuscular junction / cerebral cortex development / kinase binding / cell-cell adhesion / cell-cell junction / cell junction / synaptic vesicle / positive regulation of cytosolic calcium ion concentration / scaffold protein binding / protein-containing complex assembly / basolateral plasma membrane / protein phosphatase binding / chemical synaptic transmission / postsynaptic membrane / postsynapse / dendritic spine / postsynaptic density / neuron projection / signaling receptor binding / glutamatergic synapse / dendrite / synapse / protein-containing complex binding / protein kinase binding / endoplasmic reticulum / membrane / plasma membrane / cytosol / cytoplasm
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. ...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)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.89 Å
AuthorsSaro, D. / Vickrey, J. / Wawrzak, Z. / Kovari, L. / Spaller, M.
CitationJournal: To be Published
Title: Higher resolution crystal structure of the third PDZ domain of post synaptic PSD-95 protein.
Authors: Saro, D. / Vickrey, J. / Wawrzak, Z. / Kovari, L. / Spaller, M.
History
DepositionJun 16, 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 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Feb 14, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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


Theoretical massNumber of molelcules
Total (without water)12,7381
Polymers12,7381
Non-polymers00
Water1,09961
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)89.262, 89.262, 89.262
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number213
Space group name H-MP4132
Components on special symmetry positions
IDModelComponents
11A-12-

HOH

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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: third PDZ domain (residues 302-402)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: DLG4, DLGH4, PSD95 / Plasmid: pET / Production host: Escherichia coli (E. coli) / References: UniProt: P31016
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 61 / 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: 2.3 Å3/Da / Density % sol: 46.8 %
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: APS / Beamline: 14-BM-C / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jul 23, 2003
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.89→28.23 Å / Num. obs: 10234

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
XDSdata reduction
d*TREKdata scaling
XTALVIEWrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.89→19.96 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.933 / SU B: 5.314 / SU ML: 0.152 / Cross valid method: THROUGHOUT / σ(F): 1 / ESU R: 0.173 / ESU R Free: 0.173 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29575 485 4.8 %RANDOM
Rwork0.235 ---
obs0.23812 9630 98.82 %-
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: 38.398 Å2
Refinement stepCycle: LAST / Resolution: 1.89→19.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms827 0 0 61 888
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0360.021839
X-RAY DIFFRACTIONr_bond_other_d0.0030.02779
X-RAY DIFFRACTIONr_angle_refined_deg2.5541.9551131
X-RAY DIFFRACTIONr_angle_other_deg1.15431802
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.3185109
X-RAY DIFFRACTIONr_chiral_restr0.1540.2126
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.02960
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02173
X-RAY DIFFRACTIONr_nbd_refined0.2410.2159
X-RAY DIFFRACTIONr_nbd_other0.2770.2969
X-RAY DIFFRACTIONr_nbtor_other0.0990.2565
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2220.246
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1260.25
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3440.222
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3620.26
X-RAY DIFFRACTIONr_mcbond_it1.6751.5539
X-RAY DIFFRACTIONr_mcangle_it2.782860
X-RAY DIFFRACTIONr_scbond_it4.1563300
X-RAY DIFFRACTIONr_scangle_it6.2554.5271
LS refinement shellResolution: 1.89→1.939 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.439 31
Rwork0.349 711
Refinement TLS params.Method: refined / Origin x: 7.0666 Å / Origin y: 63.1971 Å / Origin z: 10.4466 Å
111213212223313233
T0.0345 Å20.0229 Å2-0.0181 Å2-0.0256 Å20.0037 Å2--0.0335 Å2
L1.9235 °20.2469 °20.0896 °2-0.712 °2-0.1604 °2--0.8597 °2
S0.0222 Å °-0.0393 Å °-0.1243 Å °-0.0185 Å °-0.0341 Å °-0.0452 Å °-0.0274 Å °0.031 Å °0.0119 Å °

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