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- PDB-6qjd: Crystal Structure of the truncated form of the third PDZ domain o... -

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Basic information

Entry
Database: PDB / ID: 6qjd
TitleCrystal Structure of the truncated form of the third PDZ domain of PSD-95: residues 302-392
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 / receptor localization to synapse / positive regulation of neuron projection arborization / regulation of grooming behavior / synaptic vesicle maturation / cerebellar mossy fiber ...LGI-ADAM interactions / P2Y1 nucleotide receptor binding / beta-1 adrenergic receptor binding / neuroligin family protein binding / NrCAM interactions / receptor localization to synapse / positive regulation of neuron projection arborization / regulation of grooming behavior / synaptic vesicle maturation / cerebellar mossy fiber / Synaptic adhesion-like molecules / cellular response to potassium ion / protein localization to synapse / vocalization behavior / neuron spine / AMPA glutamate receptor clustering / juxtaparanode region of axon / establishment or maintenance of epithelial cell apical/basal polarity / Trafficking of AMPA receptors / dendritic spine morphogenesis / negative regulation of receptor internalization / postsynaptic neurotransmitter receptor diffusion trapping / neuron projection terminus / RHO GTPases activate CIT / Assembly and cell surface presentation of NMDA receptors / acetylcholine receptor binding / Neurexins and neuroligins / neurotransmitter receptor localization to postsynaptic specialization membrane / Activation of Ca-permeable Kainate Receptor / cortical cytoskeleton / Signaling by ERBB4 / Negative regulation of NMDA receptor-mediated neuronal transmission / Unblocking of NMDA receptors, glutamate binding and activation / locomotory exploration behavior / regulation of NMDA receptor activity / social behavior / positive regulation of excitatory postsynaptic potential / Long-term potentiation / AMPA glutamate receptor complex / neuromuscular process controlling balance / excitatory synapse / D1 dopamine 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 / Ras activation upon Ca2+ influx through NMDA receptor / dendrite cytoplasm / synaptic membrane / learning / PDZ domain binding / postsynaptic density membrane / adherens junction / regulation of long-term neuronal synaptic plasticity / neuromuscular junction / establishment of protein localization / cell-cell adhesion / kinase binding / endocytic vesicle membrane / synaptic vesicle / cell junction / nervous system development / positive regulation of cytosolic calcium ion concentration / chemical synaptic transmission / RAF/MAP kinase cascade / scaffold protein binding / postsynaptic membrane / basolateral plasma membrane / protein phosphatase binding / protein-containing complex assembly / dendritic spine / postsynaptic density / neuron projection / synapse / glutamatergic synapse / protein-containing complex binding / 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. / 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 / 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: 1.551 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: 5OHW
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
C: Disks large homolog 4
D: Disks large homolog 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,30911
Polymers39,6374
Non-polymers6727
Water4,486249
1
A: Disks large homolog 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,1013
Polymers9,9091
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Disks large homolog 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,1013
Polymers9,9091
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Disks large homolog 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,1974
Polymers9,9091
Non-polymers2883
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Disks large homolog 4


Theoretical massNumber of molelcules
Total (without water)9,9091
Polymers9,9091
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.118, 53.968, 62.613
Angle α, β, γ (deg.)90.000, 93.250, 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: 9909.155 Da / Num. of mol.: 4 / Fragment: PDZ domain
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 / Sulfate


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 249 / 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: 2.3 Å3/Da / Density % sol: 46.59 % / Mosaicity: 0.25 °
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 6 / Details: 0.2 M ammonium sulphate, 30% PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.96864 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 16, 2014 / Details: Shutterless data collection
RadiationMonochromator: liquid nitrogen cooled channel-cut silicon monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96864 Å / Relative weight: 1
ReflectionResolution: 1.55→19.6 Å / Num. obs: 48816 / % possible obs: 94.1 % / Redundancy: 3.4 % / CC1/2: 0.983 / Rmerge(I) obs: 0.144 / Net I/σ(I): 5.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Diffraction-ID% possible all
1.55-1.583.10.48724520.729196.7
8.49-19.64.30.1262670.98180.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
Aimless0.3.11data scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3.24data extraction
XDSdata processing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3K82

3k82


Resolution: 1.551→19.6 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.01 / Phase error: 26.57
RfactorNum. reflection% reflection
Rfree0.259 2414 4.95 %
Rwork0.2161 --
obs0.2183 48788 93.21 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 73.89 Å2 / Biso mean: 17.1506 Å2 / Biso min: 4.05 Å2
Refinement stepCycle: final / Resolution: 1.551→19.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2484 0 35 251 2770
Biso mean--27.48 23.47 -
Num. residues----334
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 17

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5507-1.58230.31211470.25412795294296
1.5823-1.61670.2891660.24152730289695
1.6167-1.65430.28221590.23112702286193
1.6543-1.69570.24471380.22972793293195
1.6957-1.74150.26781420.21212778292095
1.7415-1.79270.24621380.21292785292396
1.7927-1.85050.23381450.21022763290895
1.8505-1.91660.29151400.20842792293295
1.9166-1.99330.23971270.20292723285093
1.9933-2.08390.24821290.20552792292195
2.0839-2.19360.24851260.2042744287094
2.1936-2.33090.26691350.20232740287593
2.3309-2.51050.2651660.20622702286893
2.5105-2.76250.23531630.21522682284592
2.7625-3.16080.28071460.22182669281591
3.1608-3.97680.24871220.21392602272488
3.9768-19.60320.25191250.22862582270785

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