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- PDB-5hfd: The third PDZ domain from the synaptic protein PSD-95 (G330T, H37... -

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Basic information

Entry
Database: PDB / ID: 5hfd
TitleThe third PDZ domain from the synaptic protein PSD-95 (G330T, H372A double 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 / 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: 1.6 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 (G330T, H372A double 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


Theoretical massNumber of molelcules
Total (without water)12,7151
Polymers12,7151
Non-polymers00
Water2,288127
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)89.281, 89.281, 89.281
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-592-

HOH

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Components

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


Mass: 12715.051 Da / Num. of mol.: 1 / Fragment: PDZ-3 domain (UNP residues 302-402) / Mutation: G330T 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 127 / 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: 2.14 Å3/Da / Density % sol: 42.6 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7
Details: Reservoir solution contained 1 M sodium citrate, pH 7.0. Equal amounts (1.5 microliters) of protein (13 mg/mL) and reservoir solution were mixed and equillibrated against 500 microliters of ...Details: Reservoir solution contained 1 M sodium citrate, pH 7.0. Equal amounts (1.5 microliters) of protein (13 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: 0.9793144 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 18, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793144 Å / Relative weight: 1
ReflectionResolution: 1.6→28.233 Å / Num. obs: 16618 / % possible obs: 99.85 % / Redundancy: 15.4 % / Rmerge(I) obs: 0.043 / Net I/σ(I): 63.192
Reflection shellResolution: 1.5999→1.647 Å / Redundancy: 15.7 % / Mean I/σ(I) obs: 2.111

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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: 1.6→28.233 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.49 / Phase error: 19.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1968 1662 10 %random selection
Rwork0.1811 ---
obs0.1827 16618 99.85 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.6→28.233 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms892 0 0 127 1019
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0141106
X-RAY DIFFRACTIONf_angle_d1.2571524
X-RAY DIFFRACTIONf_dihedral_angle_d18.622427
X-RAY DIFFRACTIONf_chiral_restr0.076165
X-RAY DIFFRACTIONf_plane_restr0.011220
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5999-1.6470.26591340.24621207X-RAY DIFFRACTION99
1.647-1.70020.26931340.22281205X-RAY DIFFRACTION100
1.7002-1.76090.24891380.23051228X-RAY DIFFRACTION100
1.7609-1.83140.2331350.21371225X-RAY DIFFRACTION100
1.8314-1.91470.25011350.19951214X-RAY DIFFRACTION100
1.9147-2.01570.21241370.18791235X-RAY DIFFRACTION100
2.0157-2.14190.18821380.17921232X-RAY DIFFRACTION100
2.1419-2.30720.20011360.16931232X-RAY DIFFRACTION100
2.3072-2.53930.18971390.17921255X-RAY DIFFRACTION100
2.5393-2.90640.20011400.18251263X-RAY DIFFRACTION100
2.9064-3.66050.17771440.16321278X-RAY DIFFRACTION100
3.6605-28.23750.1591520.16281382X-RAY DIFFRACTION99
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)
15.96716.10734.20376.30634.42483.39081.0897-1.9276-1.14440.8829-0.6885-0.74480.49370.165-0.36330.3887-0.0023-0.06180.57080.11430.541360.452166.99247.7965
23.8235-0.5078-0.60154.0915-0.88243.374-0.1428-0.42460.21340.39350.1026-0.0874-0.36330.13530.04090.1553-0.0344-0.01480.10530.00590.10141.27164.992240.8775
31.5355-1.02630.21885.1844-1.19341.2614-0.03370.40370.0856-0.65330.04960.2514-0.08630.06-0.05070.1734-0.0406-0.06520.17110.02460.129840.338265.325722.5442
43.00891.3088-0.55073.0309-0.1333.51360.14440.429-0.8193-0.08630.01650.45530.8521-0.21740.23950.1709-0.0955-0.06490.0485-0.0130.360337.681751.092229.8033
52.93911.7444-1.18776.9465-1.33365.46950.1505-0.03890.15760.3004-0.27620.0822-0.55230.1490.13660.086-0.0365-0.01590.08460.00650.097645.941266.812331.6941
62.4392-0.2161-0.16141.57080.94612.5524-0.01330.18010.14670.0859-0.06940.4750.1918-0.4190.06260.0738-0.057-0.00470.1480.04690.184831.670157.993533.44
75.2095-2.40420.79833.28280.40883.4839-0.18630.196-0.0171-0.44710.23460.4476-0.2131-0.22120.09640.1182-0.053-0.07810.26470.03760.149931.753558.67822.8601
82.3047-1.18190.8982.1881-0.40532.6304-0.17770.1130.1575-0.04080.12480.2456-0.3078-0.27470.01610.1192-0.0178-0.04730.10950.06180.158634.477266.348531.5113
92.0645-2.2909-2.11992.70632.36632.2018-0.5119-0.265-0.25870.64250.25680.10360.97740.02150.19890.22580.01190.0340.12560.04510.144544.449750.261937.7524
103.21011.15331.20513.74130.81895.511-0.3101-0.2150.30430.54550.3265-0.35820.22660.42970.13420.17590.088-0.06690.2208-0.04190.186453.085951.489637.6464
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 297 through 304 )
2X-RAY DIFFRACTION2chain 'A' and (resid 305 through 317 )
3X-RAY DIFFRACTION3chain 'A' and (resid 318 through 328 )
4X-RAY DIFFRACTION4chain 'A' and (resid 329 through 341 )
5X-RAY DIFFRACTION5chain 'A' and (resid 342 through 356 )
6X-RAY DIFFRACTION6chain 'A' and (resid 357 through 371 )
7X-RAY DIFFRACTION7chain 'A' and (resid 372 through 380 )
8X-RAY DIFFRACTION8chain 'A' and (resid 381 through 392 )
9X-RAY DIFFRACTION9chain 'A' and (resid 393 through 399 )
10X-RAY DIFFRACTION10chain 'A' and (resid 400 through 415 )

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