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

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Basic information

Entry
Database: PDB / ID: 6qjl
TitleCrystal Structure of the third PDZ domain of PSD-95 protein D332G mutant: space group P21
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 / NrCAM interactions / synaptic vesicle maturation / positive regulation of neuron projection arborization / regulation of grooming behavior / receptor localization to synapse / vocalization behavior ...LGI-ADAM interactions / P2Y1 nucleotide receptor binding / beta-1 adrenergic receptor binding / neuroligin family protein binding / NrCAM interactions / synaptic vesicle maturation / positive regulation of neuron projection arborization / regulation of grooming behavior / receptor localization to synapse / vocalization behavior / cerebellar mossy fiber / neuron spine / protein localization to synapse / Synaptic adhesion-like molecules / establishment or maintenance of epithelial cell apical/basal polarity / AMPA glutamate receptor clustering / cellular response to potassium ion / dendritic spine morphogenesis / Trafficking of AMPA receptors / negative regulation of receptor internalization / juxtaparanode region of axon / acetylcholine receptor binding / neuron projection terminus / RHO GTPases activate CIT / Assembly and cell surface presentation of NMDA receptors / NMDA selective glutamate receptor signaling pathway / Neurexins and neuroligins / Activation of Ca-permeable Kainate Receptor / neurotransmitter receptor localization to postsynaptic specialization membrane / cortical cytoskeleton / Negative regulation of NMDA receptor-mediated neuronal transmission / social behavior / Unblocking of NMDA receptors, glutamate binding and activation / locomotory exploration behavior / AMPA glutamate receptor complex / Signaling by ERBB4 / neuromuscular process controlling balance / Long-term potentiation / excitatory synapse / 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 / learning / PDZ domain binding / adherens junction / establishment of protein localization / synaptic membrane / regulation of long-term neuronal synaptic plasticity / postsynaptic density membrane / neuromuscular junction / cell-cell adhesion / kinase binding / endocytic vesicle membrane / cell junction / synaptic vesicle / nervous system development / positive regulation of cytosolic calcium ion concentration / RAF/MAP kinase cascade / protein-containing complex assembly / scaffold protein binding / protein phosphatase binding / chemical synaptic transmission / dendritic spine / postsynaptic membrane / neuron projection / postsynaptic density / synapse / protein-containing complex binding / protein kinase 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: 1.043 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: 5OII
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
B: Disks large homolog 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,5576
Polymers22,1812
Non-polymers3764
Water3,747208
1
A: Disks large homolog 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,2793
Polymers11,0901
Non-polymers1882
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Disks large homolog 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,2793
Polymers11,0901
Non-polymers1882
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.313, 47.023, 43.253
Angle α, β, γ (deg.)90.000, 92.190, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 11090.453 Da / Num. of mol.: 2 / 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.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 208 / 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: 1.89 Å3/Da / Density % sol: 35.01 % / Mosaicity: 0.28 °
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: 1.04→47.02 Å / Num. obs: 153886 / % possible obs: 99.3 % / Redundancy: 3.5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.049 / Rpim(I) all: 0.03 / Rrim(I) all: 0.058 / Net I/σ(I): 12
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.04-1.063.30.47538900.8650.30.56499.6
5.71-47.023.40.0394980.9970.0240.04696.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.3.6data scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3.24data extraction
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5OIH

5oih
PDB Unreleased entry


Resolution: 1.043→31.821 Å / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 0.02 / Phase error: 17.69
RfactorNum. reflection% reflection
Rfree0.1745 7713 5.01 %
Rwork0.1515 --
obs0.1527 153886 99.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 49.48 Å2 / Biso mean: 16.4975 Å2 / Biso min: 7.05 Å2
Refinement stepCycle: final / Resolution: 1.043→31.821 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1466 0 28 209 1703
Biso mean--16.07 25.54 -
Num. residues----194
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.0428-1.05470.24982520.241948475099100
1.0547-1.06710.24772880.22949065194100
1.0671-1.08010.26672570.223248885145100
1.0801-1.09370.24092690.210848135082100
1.0937-1.10810.24592450.199949365181100
1.1081-1.12330.22992480.197249005148100
1.1233-1.13940.20522140.18649825196100
1.1394-1.15640.18422230.17744866508999
1.1564-1.17440.19162640.173849575221100
1.1744-1.19370.1622480.164448315079100
1.1937-1.21430.22952170.165849785195100
1.2143-1.23640.20482890.163648525141100
1.2364-1.26010.19342730.155348525125100
1.2601-1.28590.18292810.150348735154100
1.2859-1.31380.1772430.152849305173100
1.3138-1.34440.1522320.146749265158100
1.3444-1.3780.18982580.144249235181100
1.378-1.41530.14951770.145949555132100
1.4153-1.45690.15782150.140449625177100
1.4569-1.50390.16272340.134948865120100
1.5039-1.55770.13842710.13564872514399
1.5577-1.62010.18242710.13644840511199
1.6201-1.69380.14083290.13614756508599
1.6938-1.78310.17033220.13634810513299
1.7831-1.89480.16532650.13694789505498
1.8948-2.04110.16612180.1374855507398
2.0411-2.24640.16152790.12914766504598
2.2464-2.57130.17162480.14444860510898
2.5713-3.23910.16773260.15514733505999
3.2391-31.83620.17812570.15694829508698

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