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- PDB-5hdy: The third PDZ domain from the synaptic protein PSD-95 -

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Basic information

Entry
Database: PDB / ID: 5hdy
TitleThe third PDZ domain from the synaptic protein PSD-95
ComponentsDisks large homolog 4
KeywordsPEPTIDE BINDING PROTEIN / PDZ / GLGF / DHR / adhesion / synapse / synaptic density / peptide-binding 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)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.801 Å
AuthorsWhite, K.I. / Raman, A.S. / Ranganathan, R.
Funding support United States, 1items
OrganizationGrant numberCountry
Robert A. Welch FoundationI-1366 United States
CitationJournal: To Be Published
Title: The third PDZ domain from the synaptic protein PSD-95
Authors: White, K.I. / Raman, A.S. / Ranganathan, R.
History
DepositionJan 5, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 11, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 27, 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: Disks large homolog 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,8302
Polymers12,7381
Non-polymers921
Water2,108117
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)89.657, 89.657, 89.657
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-629-

HOH

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Components

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


Mass: 12738.067 Da / Num. of mol.: 1 / Fragment: PDZ-3 domain (UNP residues 302-402)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Dlg4, Dlgh4, Psd95 / Plasmid: pGEX-4T-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P31016
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 117 / 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: 2.24 Å3/Da / Density % sol: 45.2 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.9
Details: Equal amounts (1.5 microliters) of protein (9 mg/mL) and reservoir solution were mixed and equillibrated against microliters of crystallization buffer (1.0 M sodium citrate) at 289 K. ...Details: Equal amounts (1.5 microliters) of protein (9 mg/mL) and reservoir solution were mixed and equillibrated against microliters of crystallization buffer (1.0 M sodium citrate) at 289 K. Diamond-shaped crystals appeared either spontaneously or with microseeding after 1-5 days and grew to 100-200 microns in length over several weeks.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 13, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.801→40.096 Å / Num. obs: 11131 / % possible obs: 93.23 % / Redundancy: 9.1 % / Rmerge(I) obs: 0.35 / Net I/σ(I): 52.621
Reflection shellResolution: 1.801→1.866 Å / Redundancy: 8.1 % / Mean I/σ(I) obs: 1.313

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Processing

Software
NameVersionClassification
PHENIX1.10pre_2104refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BFE

1bfe


Resolution: 1.801→40.096 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.48 / Phase error: 21.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2198 1114 10.01 %Random selection
Rwork0.1865 ---
obs0.1899 11130 93.23 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.801→40.096 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms888 0 6 117 1011
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011135
X-RAY DIFFRACTIONf_angle_d1.1611553
X-RAY DIFFRACTIONf_dihedral_angle_d17.419450
X-RAY DIFFRACTIONf_chiral_restr0.412165
X-RAY DIFFRACTIONf_plane_restr0.01220
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8014-1.88340.2963940.2861842X-RAY DIFFRACTION65
1.8834-1.98270.26891440.24291287X-RAY DIFFRACTION97
1.9827-2.10690.23551440.20781299X-RAY DIFFRACTION100
2.1069-2.26960.23361450.18771312X-RAY DIFFRACTION99
2.2696-2.4980.23891470.18771311X-RAY DIFFRACTION99
2.498-2.85940.21311450.18521310X-RAY DIFFRACTION98
2.8594-3.60210.1891460.1771313X-RAY DIFFRACTION96
3.6021-40.10570.20961490.16471342X-RAY DIFFRACTION91
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)
19.1108-0.6763.29382.25371.43322.61050.4408-1.0042-0.4620.5380.00980.06680.46110.271-0.47490.3437-0.1318-0.08360.76850.02990.760760.435966.739447.7797
24.732-3.18752.54577.217-5.0984.3988-0.2554-0.24350.15070.45850.10120.1095-0.49450.15190.10490.2379-0.00220.04320.13110.06410.164241.008466.177140.3317
34.83260.2250.46190.10920.67964.4315-0.31390.35870.039-0.21140.01760.019-0.2182-0.187-0.01380.1341-0.0724-0.09910.21440.02470.216538.839361.792124.6566
42.80711.8734-0.73964.3842-1.28472.5928-0.03870.0431-0.00480.1918-0.03440.2653-0.0114-0.0406-0.05590.085-0.0707-0.02180.1010.0670.136744.567163.226131.1067
51.0959-0.00450.20.58850.01620.7435-0.0281-0.04570.0060.08-0.02320.25830.1103-0.2403-0.33010.0039-0.11540.08320.13490.10590.318634.928759.211634.6874
61.2358-0.45670.43680.54990.65211.8853-0.10140.3128-0.025-0.2053-0.00840.59370.0569-0.38530.12330.1385-0.0631-0.06920.27960.06180.362934.409961.098229.4384
76.2944-0.49481.20096.04440.64596.2027-0.2409-0.23740.13540.46910.2643-0.22080.28330.2162-0.0140.16820.0338-0.00270.10920.04430.122851.000850.795137.0345
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 299:304)
2X-RAY DIFFRACTION2(chain A and resid 305:317)
3X-RAY DIFFRACTION3(chain A and resid 318:332)
4X-RAY DIFFRACTION4(chain A and resid 333:354)
5X-RAY DIFFRACTION5(chain A and resid 355:368)
6X-RAY DIFFRACTION6(chain A and resid 369:394)
7X-RAY DIFFRACTION7(chain A and resid 395:415)

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