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

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Basic information

Entry
Database: PDB / ID: 6qjn
TitleCrystal Structure of the third PDZ domain of PSD-95 protein D332G mutant: space group I4122
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 / positive regulation of neuron projection arborization / synaptic vesicle maturation / regulation of grooming behavior / receptor localization to synapse / cellular response to potassium ion ...LGI-ADAM interactions / P2Y1 nucleotide receptor binding / beta-1 adrenergic receptor binding / neuroligin family protein binding / NrCAM interactions / positive regulation of neuron projection arborization / synaptic vesicle maturation / regulation of grooming behavior / receptor localization to synapse / cellular response to potassium ion / protein localization to synapse / cerebellar mossy fiber / vocalization behavior / Synaptic adhesion-like molecules / neuron spine / AMPA glutamate receptor clustering / Trafficking of AMPA receptors / dendritic spine morphogenesis / juxtaparanode region of axon / establishment or maintenance of epithelial cell apical/basal polarity / negative regulation of receptor internalization / postsynaptic neurotransmitter receptor diffusion trapping / neuron projection terminus / acetylcholine receptor binding / RHO GTPases activate CIT / Assembly and cell surface presentation of NMDA receptors / Neurexins and neuroligins / regulation of NMDA receptor activity / Activation of Ca-permeable Kainate Receptor / neurotransmitter receptor localization to postsynaptic specialization membrane / cortical cytoskeleton / Negative regulation of NMDA receptor-mediated neuronal transmission / Signaling by ERBB4 / Unblocking of NMDA receptors, glutamate binding and activation / locomotory exploration behavior / extrinsic component of cytoplasmic side of plasma membrane / positive regulation of excitatory postsynaptic potential / Long-term potentiation / AMPA glutamate receptor complex / social behavior / neuromuscular process controlling balance / positive regulation of protein tyrosine kinase activity / excitatory synapse / D1 dopamine receptor binding / positive regulation of synaptic transmission / ionotropic glutamate receptor binding / Ras activation upon Ca2+ influx through NMDA receptor / dendrite cytoplasm / learning / synaptic membrane / PDZ domain binding / adherens junction / postsynaptic density membrane / regulation of long-term neuronal synaptic plasticity / establishment of protein localization / neuromuscular junction / kinase binding / cell-cell adhesion / endocytic vesicle membrane / synaptic vesicle / cell junction / nervous system development / positive regulation of cytosolic calcium ion concentration / RAF/MAP kinase cascade / scaffold protein binding / protein-containing complex assembly / chemical synaptic transmission / basolateral plasma membrane / postsynaptic membrane / protein phosphatase binding / dendritic spine / postsynaptic density / neuron projection / glutamatergic synapse / synapse / protein-containing complex binding / protein kinase binding / signal transduction / endoplasmic reticulum / 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: 1.8 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: 5OIJ
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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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


Theoretical massNumber of molelcules
Total (without water)22,1812
Polymers22,1812
Non-polymers00
Water1,49583
1
A: Disks large homolog 4


Theoretical massNumber of molelcules
Total (without water)11,0901
Polymers11,0901
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Disks large homolog 4


Theoretical massNumber of molelcules
Total (without water)11,0901
Polymers11,0901
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)89.871, 89.871, 84.814
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number98
Space group name H-MI4122
Components on special symmetry positions
IDModelComponents
11A-503-

HOH

21A-512-

HOH

31A-532-

HOH

41A-538-

HOH

51A-557-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 312 through 330 or resid 333 through 403))
21chain B

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ARGARGGLYGLY(chain A and (resid 312 through 330 or resid 333 through 403))AA312 - 33013 - 31
12GLYGLYLYSLYS(chain A and (resid 312 through 330 or resid 333 through 403))AA333 - 40334 - 104
21ARGARGLYSLYSchain BBB312 - 40313 - 104

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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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 83 / 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: 1.93 Å3/Da / Density % sol: 36.28 % / Mosaicity: 0.17 °
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 0.1 M sodium citrate, 20% 2-Propanol, 20% PEG 4000, 5% Glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.96998 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 28, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96998 Å / Relative weight: 1
ReflectionResolution: 1.8→19.85 Å / Num. obs: 16272 / % possible obs: 99.3 % / Redundancy: 4.7 % / CC1/2: 0.996 / Rmerge(I) obs: 0.078 / Rpim(I) all: 0.039 / Rrim(I) all: 0.087 / Net I/σ(I): 11.3 / Num. measured all: 77217 / Scaling rejects: 35
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
1.8-1.845.10.42747979420.8960.2050.4753.499.8
9-19.854.50.0396401420.9990.020.04519.789.4

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Phasing

PhasingMethod: molecular replacement

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Processing

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

3k82


Resolution: 1.8→19.853 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 0.18 / Phase error: 23.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2269 3071 10.23 %
Rwork0.2053 26957 -
obs0.2074 30028 97.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 116.31 Å2 / Biso mean: 41.7465 Å2 / Biso min: 13.24 Å2
Refinement stepCycle: final / Resolution: 1.8→19.853 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1390 0 0 83 1473
Biso mean---35.32 -
Num. residues----184
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A536X-RAY DIFFRACTION11.213TORSIONAL
12B536X-RAY DIFFRACTION11.213TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 22

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8001-1.82820.35451310.311712541385100
1.8282-1.85810.30031490.268312451394100
1.8581-1.89020.33541220.259212431365100
1.8902-1.92450.28161400.235912731413100
1.9245-1.96150.29731400.2481259139999
1.9615-2.00150.29721510.22821226137799
2.0015-2.0450.2731540.23211186134098
2.045-2.09250.26671570.22221213137097
2.0925-2.14470.24721660.22851203136999
2.1447-2.20270.23831630.216612251388100
2.2027-2.26740.22371640.22141212137698
2.2674-2.34050.2455980.20651288138699
2.3405-2.4240.25851300.21251257138799
2.424-2.52080.29071130.21241241135498
2.5208-2.63530.24891300.21261235136596
2.6353-2.77390.21111580.21691152131096
2.7739-2.94720.23561500.19971231138197
2.9472-3.17390.21751340.20391212134697
3.1739-3.49170.20871100.19351225133596
3.4917-3.99340.1791240.18341183130793
3.9934-5.01780.19251610.16421171133295
5.0178-19.85460.1921260.2011223134996
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)
15.48620.3771-0.12675.87052.25847.24610.1323-0.51940.1201-0.0146-0.1479-0.325-0.10060.5069-0.30390.13180.02190.02310.2240.00770.208436.674212.04612.7989
25.8636-1.7523-2.85932.1340.45482.31590.33240.134-1.5311-0.1739-0.22260.32370.1883-0.4930.26110.23980.0618-0.05140.24310.07370.313224.65232.2291-0.0912
33.561-0.9851-1.70815.34671.89096.4248-0.0485-0.4851-0.30210.06560.08180.09180.03550.1673-0.02410.14820.0299-0.00860.20560.0550.135729.0645.69546.5272
48.8892-3.83030.05174.5957-1.07144.17690.081-0.1673-0.00710.03860.08580.16350.0835-0.2196-0.1350.15780.01970.0040.1834-0.02260.122522.179714.04392.2117
53.1792-0.4776-1.78053.9909-0.28281.0313-0.0241-0.37640.0285-0.0588-0.15480.27710.2524-1.24850.12530.1169-0.0258-0.00190.3039-0.02620.187129.351510.9423-1.5302
68.79135.4752-1.17917.32641.52867.35740.4241-0.56640.05770.7698-0.2188-0.0895-0.56390.6125-0.20030.25510.0050.00280.3703-0.02270.133727.5479.420518.2189
73.6786-2.71850.78032.346-2.17227.20480.1823-1.2203-0.83890.0138-0.4059-1.14260.28270.65350.07950.4224-0.11820.01540.42640.14620.618711.7458-9.648421.7138
83.866-0.7303-0.6993.4079-1.07770.9668-0.03360.2668-0.65070.0766-0.25870.17070.18250.0180.2990.2471-0.0021-0.00170.1879-0.01710.284717.8983-3.106214.1301
94.69061.33010.12443.11111.90911.27130.205-1.59-1.09130.9861-0.52170.02570.89310.5881-0.75770.44790.0668-0.17520.3880.60610.596421.7263-6.444421.0618
104.78192.92620.86312.05511.31515.0606-0.3279-0.1434-1.90710.2080.5121-0.64361.69580.00810.36470.5067-0.04210.03090.30980.01180.770117.6925-13.639813.8117
113.2226-2.50340.44812.6902-2.86148.32260.5970.4219-2.0084-0.85740.6963-0.45120.8194-0.4109-0.82220.6691-0.29210.030.6341-0.26511.152114.1247-16.8118.6042
124.2032-0.4508-1.28932.21871.83184.3345-0.67611.8055-1.7096-0.4565-0.690.33970.6583-0.21180.51790.3236-0.1569-0.07260.66180.13040.623812.3422-8.930111.4209
135.4036-4.52433.09526.8545-1.07867.2770.7585-0.4939-1.4491-0.8788-0.9444-0.80390.84540.66890.14360.44180.29960.06110.80030.24390.647931.6374-9.505511.2182
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 307 through 317 )A307 - 317
2X-RAY DIFFRACTION2chain 'A' and (resid 318 through 328 )A318 - 328
3X-RAY DIFFRACTION3chain 'A' and (resid 329 through 356 )A329 - 356
4X-RAY DIFFRACTION4chain 'A' and (resid 357 through 380 )A357 - 380
5X-RAY DIFFRACTION5chain 'A' and (resid 381 through 392 )A381 - 392
6X-RAY DIFFRACTION6chain 'A' and (resid 393 through 403 )A393 - 403
7X-RAY DIFFRACTION7chain 'B' and (resid 312 through 317 )B312 - 317
8X-RAY DIFFRACTION8chain 'B' and (resid 318 through 350 )B318 - 350
9X-RAY DIFFRACTION9chain 'B' and (resid 351 through 356 )B351 - 356
10X-RAY DIFFRACTION10chain 'B' and (resid 357 through 362 )B357 - 362
11X-RAY DIFFRACTION11chain 'B' and (resid 363 through 371 )B363 - 371
12X-RAY DIFFRACTION12chain 'B' and (resid 372 through 392 )B372 - 392
13X-RAY DIFFRACTION13chain 'B' and (resid 393 through 403 )B393 - 403

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