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- PDB-1tp5: Crystal structure of PDZ3 domain of PSD-95 protein complexed with... -

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Basic information

Entry
Database: PDB / ID: 1tp5
TitleCrystal structure of PDZ3 domain of PSD-95 protein complexed with a peptide ligand KKETWV
Components
  • LYS-LYS-GLU-THR-TRP-VAL peptide ligand
  • Presynaptic density protein 95
KeywordsPEPTIDE BINDING PROTEIN / PDZ-peptide ligand complex
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 / beta-1 adrenergic receptor binding / Neurexins and neuroligins / neuroligin family protein binding / receptor localization to synapse / positive regulation of neuron projection arborization / regulation of grooming behavior ...RHO GTPases activate CIT / positive regulation of AMPA glutamate receptor clustering / neuronal ion channel clustering / P2Y1 nucleotide receptor binding / beta-1 adrenergic receptor binding / Neurexins and neuroligins / neuroligin family protein binding / receptor localization to synapse / positive regulation of neuron projection arborization / regulation of grooming behavior / structural constituent of postsynaptic density / synaptic vesicle maturation / proximal dendrite / AMPA glutamate receptor clustering / cerebellar mossy fiber / protein localization to synapse / cellular response to potassium ion / vocalization behavior / LGI-ADAM interactions / neuron spine / Trafficking of AMPA receptors / dendritic branch / Activation of Ca-permeable Kainate Receptor / juxtaparanode region of axon / neuron projection terminus / establishment or maintenance of epithelial cell apical/basal polarity / dendritic spine morphogenesis / negative regulation of receptor internalization / postsynaptic neurotransmitter receptor diffusion trapping / frizzled binding / dendritic spine organization / acetylcholine receptor binding / positive regulation of synapse assembly / RAF/MAP kinase cascade / Synaptic adhesion-like molecules / neurotransmitter receptor localization to postsynaptic specialization membrane / positive regulation of dendrite morphogenesis / beta-2 adrenergic receptor binding / regulation of neuronal synaptic plasticity / locomotory exploration behavior / cortical cytoskeleton / regulation of NMDA receptor activity / social behavior / positive regulation of excitatory postsynaptic potential / AMPA glutamate receptor complex / kinesin binding / neuromuscular process controlling balance / excitatory synapse / D1 dopamine receptor binding / Unblocking of NMDA receptors, glutamate binding and activation / glutamate receptor binding / positive regulation of protein tyrosine kinase activity / positive regulation of synaptic transmission / ionotropic glutamate receptor binding / extrinsic component of cytoplasmic side of plasma membrane / dendrite cytoplasm / synaptic membrane / PDZ domain binding / cell periphery / postsynaptic density membrane / regulation of long-term neuronal synaptic plasticity / neuromuscular junction / establishment of protein localization / cell-cell adhesion / cerebral cortex development / kinase binding / cell-cell junction / synaptic vesicle / cell junction / positive regulation of cytosolic calcium ion concentration / chemical synaptic transmission / postsynaptic membrane / postsynapse / scaffold protein binding / basolateral plasma membrane / protein-containing complex assembly / protein phosphatase binding / dendritic spine / postsynaptic density / neuron projection / signaling receptor binding / dendrite / glutamatergic synapse / 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. / 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)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.54 Å
AuthorsSaro, D. / Wawrzak, Z. / Martin, P. / Vickrey, J. / Paredes, A. / Kovari, L. / Spaller, M.
CitationJournal: To be Published
Title: Structure of the third PDZ domain of PSD-95 protein complexed with KKETWV peptide ligand
Authors: Saro, D. / Wawrzak, Z. / Martin, P. / Vickrey, J. / Paredes, A. / Kovari, L. / Spaller, M.
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 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Aug 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: LYS-LYS-GLU-THR-TRP-VAL peptide ligand


Theoretical massNumber of molelcules
Total (without water)13,5302
Polymers13,5302
Non-polymers00
Water3,369187
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area910 Å2
ΔGint-3 kcal/mol
Surface area6780 Å2
MethodPISA
2
A: Presynaptic density protein 95
B: LYS-LYS-GLU-THR-TRP-VAL peptide ligand

A: Presynaptic density protein 95
B: LYS-LYS-GLU-THR-TRP-VAL peptide ligand


Theoretical massNumber of molelcules
Total (without water)27,0604
Polymers27,0604
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation14_555-y+3/4,-x+3/4,-z+3/41
Buried area3760 Å2
ΔGint-14 kcal/mol
Surface area11610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.978, 89.978, 89.978
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-185-

HOH

21A-188-

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) / Plasmid: pET32 / Production host: Escherichia coli (E. coli) / References: UniProt: P31016
#2: Protein/peptide LYS-LYS-GLU-THR-TRP-VAL peptide ligand


Mass: 791.933 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: the peptide was chemically synthesized
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 187 / 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: 48 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 6.9
Details: 1.0 M sodium citrate, 0.1 M HEPES, 10 mM sodium chloride, pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 288K

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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: 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: 1.54→30 Å / Num. obs: 18320 / % possible obs: 96.2 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 1.54→1.63 Å / % possible all: 95.1

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
XDSdata reduction
XDSdata scaling
XTALVIEWrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1BE9

1be9


Resolution: 1.54→19.65 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.944 / SU B: 1.611 / SU ML: 0.059 / Cross valid method: THROUGHOUT / σ(F): 1 / ESU R: 0.089 / ESU R Free: 0.092 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22926 953 5.2 %RANDOM
Rwork0.19099 ---
obs0.1929 17356 96.4 %-
all-17356 --
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: 16.235 Å2
Refinement stepCycle: LAST / Resolution: 1.54→19.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms919 0 0 187 1106
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.021932
X-RAY DIFFRACTIONr_bond_other_d0.0030.02859
X-RAY DIFFRACTIONr_angle_refined_deg1.5581.9551254
X-RAY DIFFRACTIONr_angle_other_deg0.90731991
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8235119
X-RAY DIFFRACTIONr_chiral_restr0.0880.2139
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021060
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02188
X-RAY DIFFRACTIONr_nbd_refined0.240.2187
X-RAY DIFFRACTIONr_nbd_other0.2680.21030
X-RAY DIFFRACTIONr_nbtor_other0.0850.2604
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2050.2116
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3390.223
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3830.255
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2510.226
X-RAY DIFFRACTIONr_mcbond_it1.0721.5594
X-RAY DIFFRACTIONr_mcangle_it1.9622945
X-RAY DIFFRACTIONr_scbond_it2.8423338
X-RAY DIFFRACTIONr_scangle_it4.6944.5309
LS refinement shellResolution: 1.541→1.58 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.293 71
Rwork0.24 1246
Refinement TLS params.Method: refined / Origin x: 26.9351 Å / Origin y: 55.2517 Å / Origin z: 37.575 Å
111213212223313233
T0.0051 Å20.0013 Å20.003 Å2-0.0055 Å20.0032 Å2--0.0029 Å2
L0.0796 °20.0516 °20.0836 °2-0.2815 °2-0.0695 °2--0.1426 °2
S-0.0094 Å °-0.0013 Å °-0.0091 Å °0.0066 Å °-0.0008 Å °-0.0167 Å °-0.0141 Å °-0.0098 Å °0.0102 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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