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- PDB-5hf4: The third PDZ domain from the synaptic protein PSD-95 (H372A mutant) -

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Basic information

Entry
Database: PDB / ID: 5hf4
TitleThe third PDZ domain from the synaptic protein PSD-95 (H372A mutant)
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 / 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: 1.75 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 (H372A mutant)
Authors: White, K.I. / Raman, A.S. / Ranganathan, R.
History
DepositionJan 6, 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)12,7632
Polymers12,6711
Non-polymers921
Water2,000111
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)89.254, 89.254, 89.254
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-615-

HOH

21A-683-

HOH

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Components

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


Mass: 12670.998 Da / Num. of mol.: 1 / Fragment: PDZ-3 domain (UNP residues 302-402) / Mutation: H372A
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 / Glycerol


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


Mass: 18.015 Da / Num. of mol.: 111 / 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: 2.34 Å3/Da / Density % sol: 47.39 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7
Details: Reservoir solution contained 0.95 M sodium citrate, pH 7.0. Equal amounts (1.5 microliters) of protein (9 mg/mL) and reservoir solution were mixed and equillibrated against 500 microliters ...Details: Reservoir solution contained 0.95 M sodium citrate, pH 7.0. Equal amounts (1.5 microliters) of protein (9 mg/mL) and reservoir solution were mixed and equillibrated against 500 microliters of crystallization buffer.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9792062 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 15, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792062 Å / Relative weight: 1
ReflectionResolution: 1.75→39.916 Å / Num. obs: 12757 / % possible obs: 99.63 % / Redundancy: 11.4 % / Rmerge(I) obs: 0.045 / Net I/σ(I): 48.917
Reflection shellResolution: 1.7501→1.8201 Å / Redundancy: 11 % / Mean I/σ(I) obs: 2.286

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Processing

Software
NameVersionClassification
PHENIXdev_2026refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BFE

1bfe


Resolution: 1.75→39.916 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.47 / Phase error: 21.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2207 1279 10.03 %random selection
Rwork0.1822 ---
obs0.1861 12757 99.63 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.75→39.916 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms889 0 6 111 1006
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051071
X-RAY DIFFRACTIONf_angle_d0.9281459
X-RAY DIFFRACTIONf_dihedral_angle_d13.841420
X-RAY DIFFRACTIONf_chiral_restr0.047155
X-RAY DIFFRACTIONf_plane_restr0.004206
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7501-1.82010.2871370.25761206X-RAY DIFFRACTION97
1.8201-1.9030.29111380.22651238X-RAY DIFFRACTION100
1.903-2.00330.28471390.20451259X-RAY DIFFRACTION100
2.0033-2.12880.20681390.19271242X-RAY DIFFRACTION100
2.1288-2.29320.24161400.1771264X-RAY DIFFRACTION100
2.2932-2.52390.24311410.18471269X-RAY DIFFRACTION100
2.5239-2.8890.22971410.1861278X-RAY DIFFRACTION100
2.889-3.63950.20581470.17131310X-RAY DIFFRACTION100
3.6395-39.9260.18081570.16381412X-RAY DIFFRACTION100
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)
16.46440.83772.89616.39371.76366.28140.1981-0.7613-0.57780.80890.0297-0.2990.02890.489-0.18840.5107-0.0840.08430.5918-0.10160.783460.395166.3347.7709
22.9052-0.51180.05144.2966-1.3385.1059-0.31130.08730.25590.36790.0220.324-0.74780.2191-0.08020.1502-0.0513-0.00140.12630.06130.1940.442367.251734.7661
33.04810.7436-0.56013.30910.09883.4282-0.060.0623-0.1337-0.2136-0.06120.52740.0643-0.1111-0.08650.0724-0.0308-0.02940.09810.02650.197142.075560.877628.7387
41.4935-0.3057-0.98213.41250.80312.613-0.22360.0226-0.04550.22790.22470.55870.2055-0.13210.05830.0812-0.03150.02290.10520.06640.196641.083357.241133.5911
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 298:304)
2X-RAY DIFFRACTION2(chain A and resid 305:321)
3X-RAY DIFFRACTION3(chain A and resid 322:352)
4X-RAY DIFFRACTION4(chain A and resid 353:415)

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