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- PDB-6qji: Crystal Structure of the third PDZ domain of PSD-95 protein: spac... -

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Basic information

Entry
Database: PDB / ID: 6qji
TitleCrystal Structure of the third PDZ domain of PSD-95 protein: space group P3112
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 / juxtaparanode region of axon / acetylcholine receptor binding / neuron projection terminus / 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 / D1 dopamine receptor binding / positive regulation of synaptic transmission / 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 / regulation of long-term neuronal synaptic plasticity / cell-cell adhesion / 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 / chemical synaptic transmission / dendritic spine / postsynaptic membrane / neuron projection / postsynaptic density / synapse / protein kinase binding / protein-containing complex binding / glutamatergic synapse / endoplasmic reticulum / signal transduction / 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. ...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: 1.5 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: 5OIB
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

Downloads & links

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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
E: Disks large homolog 4
F: Disks large homolog 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,73414
Polymers63,9666
Non-polymers7698
Water8,539474
1
A: Disks large homolog 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,7572
Polymers10,6611
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Disks large homolog 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,8533
Polymers10,6611
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)10,8533
Polymers10,6611
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Disks large homolog 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,7572
Polymers10,6611
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Disks large homolog 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,7572
Polymers10,6611
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Disks large homolog 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,7572
Polymers10,6611
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.970, 61.970, 228.365
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number151
Space group name H-MP3112
Components on special symmetry positions
IDModelComponents
11B-673-

HOH

21B-685-

HOH

31E-674-

HOH

41F-669-

HOH

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Components

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


Mass: 10660.919 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DLG4, PSD95 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P78352
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 474 / 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 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / 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: ID14-4 / Wavelength: 0.9393 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 4, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9393 Å / Relative weight: 1
ReflectionResolution: 1.5→19.97 Å / Num. obs: 80715 / % possible obs: 99.6 % / Redundancy: 7.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.072 / Rpim(I) all: 0.026 / Rrim(I) all: 0.077 / Net I/σ(I): 16.6 / Num. measured all: 618089 / Scaling rejects: 133
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
1.5-1.537.30.3282881639510.9410.130.3535.1100
8.22-19.9712.60.04356274470.9980.0130.04627.782.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIXrefinement
XDSdata reduction
Aimless0.5.32data scaling
PHASERphasing
PDB_EXTRACT3.24data extraction
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3K82

3k82


Resolution: 1.5→19.972 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 0.08 / Phase error: 26.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2614 7613 4.88 %
Rwork0.2119 148439 -
obs0.2143 156052 99.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 69.42 Å2 / Biso mean: 23.5923 Å2 / Biso min: 6.43 Å2
Refinement stepCycle: final / Resolution: 1.5→19.972 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4184 0 40 475 4699
Biso mean--38.25 30.58 -
Num. residues----555
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 (%)
1.5-1.51710.30542640.251849785242100
1.5171-1.53490.3212600.262949535213100
1.5349-1.55360.32852690.261850415310100
1.5536-1.57330.33342080.253849605168100
1.5733-1.5940.35232680.245149485216100
1.594-1.61580.27273060.228349525258100
1.6158-1.63890.29072700.222149805250100
1.6389-1.66330.30262820.22849415223100
1.6633-1.68930.30572380.222750105248100
1.6893-1.7170.27592420.228949875229100
1.717-1.74660.27642940.221848805174100
1.7466-1.77830.28922540.22350505304100
1.7783-1.81250.32832580.225949235181100
1.8125-1.84950.30512600.228249845244100
1.8495-1.88960.2622500.2149835233100
1.8896-1.93360.27082420.202349955237100
1.9336-1.98190.22882640.200449035167100
1.9819-2.03540.2612690.190949355204100
2.0354-2.09520.23852230.19944974519799
2.0952-2.16280.2472200.19344973519399
2.1628-2.240.24582810.20244939522099
2.24-2.32960.23142950.19224886518199
2.3296-2.43540.25292760.19674898517499
2.4354-2.56360.25322350.20524969520499
2.5636-2.72380.27161720.20474998517099
2.7238-2.93350.25482440.20064946519099
2.9335-3.22760.22032280.1984935516399
3.2276-3.69210.20472600.1964939519999
3.6921-4.6420.22792390.19464896513598
4.642-19.97370.37062420.29544683492594

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