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- PDB-6qjk: Crystal Structure of the third PDZ domain of PSD-95 protein D332G... -

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Basic information

Entry
Database: PDB / ID: 6qjk
TitleCrystal Structure of the third PDZ domain of PSD-95 protein D332G mutant: space group P43
ComponentsDisks large homolog 4
KeywordsSIGNALING PROTEIN / pdz domain
Function / homology
Function and homology information


LGI-ADAM interactions / P2Y1 nucleotide receptor binding / beta-1 adrenergic receptor binding / neuroligin family protein binding / regulation of grooming behavior / NrCAM interactions / synaptic vesicle maturation / positive regulation of neuron projection arborization / receptor localization to synapse / vocalization behavior ...LGI-ADAM interactions / P2Y1 nucleotide receptor binding / beta-1 adrenergic receptor binding / neuroligin family protein binding / regulation of grooming behavior / NrCAM interactions / synaptic vesicle maturation / positive regulation of neuron projection arborization / receptor localization to synapse / vocalization behavior / neuron spine / cerebellar mossy fiber / AMPA glutamate receptor clustering / Synaptic adhesion-like molecules / protein localization to synapse / establishment or maintenance of epithelial cell apical/basal polarity / Trafficking of AMPA receptors / dendritic spine morphogenesis / negative regulation of receptor internalization / neuron projection terminus / juxtaparanode region of axon / acetylcholine receptor binding / RHO GTPases activate CIT / cellular response to potassium ion / Assembly and cell surface presentation of NMDA receptors / NMDA selective glutamate receptor signaling pathway / Neurexins and neuroligins / Activation of Ca-permeable Kainate Receptor / neuromuscular process controlling balance / neurotransmitter receptor localization to postsynaptic specialization membrane / cortical cytoskeleton / Negative regulation of NMDA receptor-mediated neuronal transmission / Unblocking of NMDA receptors, glutamate binding and activation / locomotory exploration behavior / AMPA glutamate receptor complex / Signaling by ERBB4 / Long-term potentiation / excitatory synapse / social behavior / positive regulation of excitatory postsynaptic potential / positive regulation of synaptic transmission / D1 dopamine receptor binding / regulation of postsynaptic membrane neurotransmitter receptor levels / ionotropic glutamate receptor binding / dendrite cytoplasm / Ras activation upon Ca2+ influx through NMDA receptor / synaptic membrane / learning / adherens junction / PDZ domain binding / neuromuscular junction / establishment of protein localization / cell-cell adhesion / regulation of long-term neuronal synaptic plasticity / postsynaptic density membrane / kinase binding / synaptic vesicle / endocytic vesicle membrane / cell junction / nervous system development / positive regulation of cytosolic calcium ion concentration / RAF/MAP kinase cascade / protein-containing complex assembly / scaffold protein binding / protein phosphatase binding / dendritic spine / chemical synaptic transmission / postsynaptic membrane / neuron projection / postsynaptic density / synapse / protein kinase binding / protein-containing complex binding / glutamatergic synapse / endoplasmic reticulum / signal transduction / 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 / 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 / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Disks large homolog 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.046 Å
AuthorsCamara-Artigas, A.
Funding support Spain, 1items
OrganizationGrant numberCountry
Spanish Ministry of Economy and CompetitivenessBIO2016-78020-R Spain
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Conformational changes in the third PDZ domain of the neuronal postsynaptic density protein 95.
Authors: Camara-Artigas, A. / Murciano-Calles, J. / Martinez, J.C.
History
DepositionJan 24, 2019Deposition site: PDBE / Processing site: PDBE
SupersessionApr 17, 2019ID: 5OIH
Revision 1.0Apr 17, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 24, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jan 24, 2024Group: 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

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Assembly

Deposited unit
A: Disks large homolog 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,7913
Polymers10,6031
Non-polymers1882
Water1,874104
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area420 Å2
ΔGint-14 kcal/mol
Surface area5530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.854, 42.854, 46.909
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number78
Space group name H-MP43

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Components

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


Mass: 10602.883 Da / Num. of mol.: 1 / Fragment: PDZ domain / Mutation: D332G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DLG4, PSD95 / Plasmid: pBAT4 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P78352
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 104 / 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: 2.03 Å3/Da / Density % sol: 39.44 % / Mosaicity: 0.25 °
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.17 M ammonium sulphate , 25.5% PEG 8000 , 15% Glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 17, 2014 / Details: sample-detector distance: adjustable 123-1356mm
RadiationMonochromator: Channel-cut double crystal monochromator (CINEL), cryocooled, 6mm gap
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.05→19.49 Å / Num. obs: 38212 / % possible obs: 95.4 % / Redundancy: 3.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.042 / Rpim(I) all: 0.025 / Rrim(I) all: 0.049 / Net I/σ(I): 13.2 / Num. measured all: 141760 / Scaling rejects: 14
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.05-1.063.70.522697218880.760.3060.6072.292.3
5.63-19.493.80.0259962640.9990.0140.0293596.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
Aimless0.3.6data scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3K82

3k82


Resolution: 1.046→19.49 Å / SU ML: 0.09 / Cross valid method: THROUGHOUT / σ(F): 0.14 / Phase error: 13.55 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1452 3591 4.78 %
Rwork0.1376 71552 -
obs0.138 75143 95.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 51.45 Å2 / Biso mean: 15.1078 Å2 / Biso min: 5.77 Å2
Refinement stepCycle: final / Resolution: 1.046→19.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms730 0 14 104 848
Biso mean--8.7 28.52 -
Num. residues----97
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 26

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.0461-1.05990.28311000.22152622272292
1.0599-1.07440.17281240.20592781290593
1.0744-1.08980.2147980.19242667276592
1.0898-1.1060.20381520.17722661281394
1.106-1.12330.17461860.16892649283593
1.1233-1.14170.19361500.15282671282194
1.1417-1.16140.1711200.1472787290795
1.1614-1.18250.17271620.14382645280794
1.1825-1.20530.11821080.13522763287194
1.2053-1.22990.16881320.14552695282794
1.2299-1.25660.15291420.13762778292095
1.2566-1.28580.16981560.13062710286695
1.2858-1.3180.13371580.12712726288496
1.318-1.35360.13991140.12852797291196
1.3536-1.39340.14881950.12572744293996
1.3934-1.43840.13021280.12642753288197
1.4384-1.48980.13021140.1192796291096
1.4898-1.54940.14051630.12162809297296
1.5494-1.61990.13231460.12162762290897
1.6199-1.70530.13231660.12312778294497
1.7053-1.8120.14011160.12542860297697
1.812-1.95180.1541450.1262786293197
1.9518-2.1480.131220.13572777289996
2.148-2.45830.1325940.13192886298099
2.4583-3.09520.14671390.14572825296498
3.0952-19.49340.13631610.14092824298598

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