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- PDB-6qjg: Crystal Structure of the third PDZ domain of PSD-95 protein D332P... -

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Basic information

Entry
Database: PDB / ID: 6qjg
TitleCrystal Structure of the third PDZ domain of PSD-95 protein D332P mutant: space group C121, structure 2
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 / AMPA glutamate receptor clustering ...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 / AMPA glutamate receptor clustering / cellular response to potassium ion / cerebellar mossy fiber / Synaptic adhesion-like molecules / protein localization to synapse / vocalization behavior / neuron spine / juxtaparanode region of axon / neuron projection terminus / Trafficking of AMPA receptors / establishment or maintenance of epithelial cell apical/basal polarity / dendritic spine morphogenesis / negative regulation of receptor internalization / postsynaptic neurotransmitter receptor diffusion trapping / 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 / locomotory exploration behavior / cortical cytoskeleton / Signaling by ERBB4 / Negative regulation of NMDA receptor-mediated neuronal transmission / Unblocking of NMDA receptors, glutamate binding and activation / regulation of NMDA receptor activity / social behavior / positive regulation of excitatory postsynaptic potential / AMPA glutamate receptor complex / Long-term potentiation / 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 / dendrite cytoplasm / Ras activation upon Ca2+ influx through NMDA receptor / 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-containing complex assembly / protein phosphatase binding / dendritic spine / postsynaptic density / neuron projection / glutamatergic synapse / 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: 2.003 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: 5OI6
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 15, 2020Group: Data collection / Category: diffrn_source
Item: _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.type
Revision 1.3Jan 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


Theoretical massNumber of molelcules
Total (without water)44,5224
Polymers44,5224
Non-polymers00
Water2,594144
1
A: Disks large homolog 4


Theoretical massNumber of molelcules
Total (without water)11,1311
Polymers11,1311
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Disks large homolog 4


Theoretical massNumber of molelcules
Total (without water)11,1311
Polymers11,1311
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Disks large homolog 4


Theoretical massNumber of molelcules
Total (without water)11,1311
Polymers11,1311
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Disks large homolog 4


Theoretical massNumber of molelcules
Total (without water)11,1311
Polymers11,1311
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)139.594, 33.501, 96.424
Angle α, β, γ (deg.)90.000, 128.930, 90.000
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 11130.517 Da / Num. of mol.: 4 / Fragment: PDZ domain / Mutation: D332P
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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 144 / 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: 1.97 Å3/Da / Density % sol: 37.55 % / Mosaicity: 0.23 °
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.1 M MES, 30 % PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.965 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Feb 25, 2015
RadiationMonochromator: Diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.965 Å / Relative weight: 1
ReflectionResolution: 2→19.44 Å / Num. obs: 23033 / % possible obs: 96.7 % / Redundancy: 2.7 % / CC1/2: 0.997 / Rmerge(I) obs: 0.053 / Rpim(I) all: 0.038 / Rrim(I) all: 0.066 / Net I/σ(I): 13.4 / Num. measured all: 62417 / Scaling rejects: 14
Reflection shell

Diffraction-ID: 1 / Redundancy: 2.8 %

Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2-2.050.43817420.8120.3140.54299.2
8.96-19.440.0222490.9990.0150.02782.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
Aimless0.5.8data scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3.24data extraction
Cootmodel building
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3K82

3k82


Resolution: 2.003→19.439 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1 / Phase error: 25.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2458 1149 4.99 %
Rwork0.1989 21874 -
obs0.2013 23023 96.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 182.01 Å2 / Biso mean: 44.9673 Å2 / Biso min: 16.58 Å2
Refinement stepCycle: final / Resolution: 2.003→19.439 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2932 0 0 144 3076
Biso mean---40.02 -
Num. residues----388
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.0027-2.09370.30361560.28512771292798
2.0937-2.2040.31471300.27452741287198
2.204-2.34190.32351360.25892666280296
2.3419-2.52230.30131340.2542765289998
2.5223-2.77550.28611470.23252786293398
2.7755-3.17560.24521580.21542715287397
3.1756-3.99520.26311320.16922720285295
3.9952-19.43960.17361560.14622710286692
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)
17.51380.3996-1.76761.1402-2.10084.03330.2179-0.84161.225-0.7038-0.58590.8673-1.6745-0.4699-0.21480.59420.0913-0.09220.3305-0.140.6127-16.3443.930234.0431
20.91721.56350.3678.5411-0.69020.4694-0.0806-0.5890.37110.43720.65521.314-0.0264-0.36650.25610.30620.04600.422-0.00460.2472-14.5705-9.619438.013
31.7054-0.5330.05470.58150.91121.88910.01820.0364-0.09860.17920.0379-0.02560.00840.05020.00020.2745-0.0047-0.03420.19980.03540.2324-10.7232-11.250224.7209
40.0617-0.08880.15911.6035-1.12370.95020.0915-0.9823-0.84081.4222-0.29220.1929-0.2795-0.47730.00350.3491-0.0229-0.02490.31290.00730.3253-22.7744-14.59230.1953
50.21070.34790.09810.75610.03260.1627-0.14740.5353-0.08760.6592-0.36580.2222-1.0436-0.8366-0.00330.37390.06040.03240.398-0.01460.3591-19.4267-5.818830.6706
60.3634-0.1717-0.14860.198-0.06620.1969-0.0791-0.82390.4425-0.02660.2377-0.4039-0.0209-0.02590.00090.28950.00490.00340.2668-0.01320.2573-8.1289-5.568531.27
70.4287-0.41460.01880.49260.16160.292-0.2064-0.65880.09790.00540.3920.3734-0.10050.23130.00020.31330.02690.00980.42330.02740.3616-1.3227-7.613331.5092
80.3062-0.4379-0.41270.62660.59370.5735-0.7168-0.1148-0.1304-0.0280.4749-0.45160.75720.13450.00070.26940.00020.00590.24630.01960.4206-3.4446-15.433325.9538
91.9622-0.1683-0.13470.38830.44451.27970.2043-0.15990.0384-0.3966-0.2963-0.13780.39990.30820.00020.40560.02280.01160.27650.03410.2618-10.4743-10.901434.6783
100.4063-0.3923-0.17290.8213-0.19080.4076-0.607-0.05850.14230.15150.04480.2124-0.7719-0.1656-0.00070.41430.0056-0.05350.27470.01750.3098-11.63440.364319.8269
111.3517-0.28270.66260.3432-0.62071.13290.3907-0.39670.03760.07810.2312-0.3988-0.0960.27760.09340.7376-0.02850.32370.3625-0.1060.6465-21.604113.82258.4128
121.4975-0.6622-1.7312.83882.00222.6098-0.31890.85660.386-0.827-0.43160.8096-0.6069-0.1611-0.17360.32720.0479-0.03260.41670.20290.4404-26.10963.480749.409
130.03020.1626-0.02190.8844-0.06870.029-0.0598-0.14810.04720.15230.0968-0.33170.29270.015-00.26270.00620.01130.2970.00890.2641-17.7411-5.924950.2888
141.7903-0.0417-1.04912.06180.95990.96060.2544-0.19710.15460.09950.12750.1748-0.20390.55290.00050.19310.00340.00030.2574-0.0570.2504-15.7663-1.064156.0364
150.5742-0.43961.10870.4591-0.60392.68730.5161-0.40260.0257-0.3736-0.15560.20620.0414-0.69030.0790.22280.01470.09570.2135-0.04310.3746-16.75696.263552.533
160.716-0.4786-0.33651.0470.20970.95940.301-0.05030.15610.45510.04410.3762-0.2205-0.12160.01390.20990.0150.04950.31820.00870.3222-25.6889-0.959561.7393
170.48970.4149-0.0360.39970.08880.2474-0.40720.1696-0.13790.44680.3755-0.28590.32390.64050.00010.30020.0416-0.00020.3317-0.00550.2648-21.9894-10.130360.3011
180.914-0.5091-1.12680.99550.12761.62090.060.38780.23650.18750.16050.4229-0.0787-0.30810.00050.23340.01720.04010.37820.06580.2886-25.4236-0.480953.5281
190.57470.30740.30660.7383-0.14490.31450.0511-0.30050.0210.27220.2968-0.26430.17170.47490.00050.3744-0.01090.01350.4029-0.07390.413-11.6124.583565.5348
201.15160.3312-1.06350.4231-0.67991.37530.350.3515-0.2136-0.2163-0.143-0.1732-0.2194-0.27260.00720.35210.024-0.00470.4323-0.05280.2916-17.1293-13.45743.1811
212.71440.19591.2541.65761.8862.48180.24990.18450.013-0.0002-0.23760.0747-0.26430.021500.25550.0393-0.0330.2354-0.01070.2426-18.1188-13.710911.4878
221.74130.402-0.97542.61450.61582.0767-0.06640.4104-0.56030.0215-0.2061-0.01170.2651-0.15740.00010.34520.00270.01050.3322-0.07220.346-17.9942-22.72187.518
230.7979-0.60530.36840.4788-0.4310.67640.3252-0.53310.22050.3770.08270.10660.1336-0.44690.00580.2473-0.01440.0310.2981-0.03370.1645-28.3078-12.426817.3099
243.0175-1.4117-0.67324.73221.07670.8477-0.3301-0.09920.24240.55420.296-0.12140.01280.0485-0.02150.31790.019-0.01890.3465-0.01770.2555-0.6719-12.974157.8602
250.6666-0.0918-0.65461.5743-0.38760.974-0.2338-0.4720.67840.76890.4521-0.4748-0.07510.17790.00450.3130.0891-0.05870.3292-0.11310.3906-1.4395-6.996662.8482
263.0124-1.5425-2.10142.76170.30283.4629-0.30360.13440.01650.09010.1876-0.06120.9269-0.01110.01410.29550.0255-0.00610.2764-0.01540.2485-1.9176-18.28355.2389
270.0572-0.14040.11540.68770.0120.34310.14720.37180.5660.0415-0.6709-0.9552-0.18820.3365-0.01810.27550.04190.0480.43410.09390.557-1.3244-2.246347.5807
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 306 through 311 )A306 - 311
2X-RAY DIFFRACTION2chain 'A' and (resid 312 through 317 )A312 - 317
3X-RAY DIFFRACTION3chain 'A' and (resid 318 through 341 )A318 - 341
4X-RAY DIFFRACTION4chain 'A' and (resid 342 through 349 )A342 - 349
5X-RAY DIFFRACTION5chain 'A' and (resid 350 through 356 )A350 - 356
6X-RAY DIFFRACTION6chain 'A' and (resid 357 through 362 )A357 - 362
7X-RAY DIFFRACTION7chain 'A' and (resid 363 through 371 )A363 - 371
8X-RAY DIFFRACTION8chain 'A' and (resid 372 through 380 )A372 - 380
9X-RAY DIFFRACTION9chain 'A' and (resid 381 through 392 )A381 - 392
10X-RAY DIFFRACTION10chain 'A' and (resid 393 through 402 )A393 - 402
11X-RAY DIFFRACTION11chain 'B' and (resid 307 through 311 )B307 - 311
12X-RAY DIFFRACTION12chain 'B' and (resid 312 through 317 )B312 - 317
13X-RAY DIFFRACTION13chain 'B' and (resid 318 through 328 )B318 - 328
14X-RAY DIFFRACTION14chain 'B' and (resid 329 through 350 )B329 - 350
15X-RAY DIFFRACTION15chain 'B' and (resid 351 through 356 )B351 - 356
16X-RAY DIFFRACTION16chain 'B' and (resid 357 through 371 )B357 - 371
17X-RAY DIFFRACTION17chain 'B' and (resid 372 through 380 )B372 - 380
18X-RAY DIFFRACTION18chain 'B' and (resid 381 through 392 )B381 - 392
19X-RAY DIFFRACTION19chain 'B' and (resid 393 through 402 )B393 - 402
20X-RAY DIFFRACTION20chain 'C' and (resid 306 through 324 )C306 - 324
21X-RAY DIFFRACTION21chain 'C' and (resid 325 through 356 )C325 - 356
22X-RAY DIFFRACTION22chain 'C' and (resid 357 through 392 )C357 - 392
23X-RAY DIFFRACTION23chain 'C' and (resid 393 through 403 )C393 - 403
24X-RAY DIFFRACTION24chain 'D' and (resid 307 through 336 )D307 - 336
25X-RAY DIFFRACTION25chain 'D' and (resid 337 through 356 )D337 - 356
26X-RAY DIFFRACTION26chain 'D' and (resid 357 through 392 )D357 - 392
27X-RAY DIFFRACTION27chain 'D' and (resid 393 through 403 )D393 - 403

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