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- PDB-6spv: Crystal structure of PDZ1-2 from PSD-95 -

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Basic information

Entry
Database: PDB / ID: 6spv
TitleCrystal structure of PDZ1-2 from PSD-95
ComponentsDisks large homolog 4
KeywordsSTRUCTURAL PROTEIN / PSD-95 fragment / clustering / protein-complex / receptor-binding / membrane associated
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 / regulation of long-term neuronal synaptic plasticity / synaptic membrane / 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 / Pdz3 Domain / 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 / Roll / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
GLUTATHIONE / Disks large homolog 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.04 Å
AuthorsRodzli, N. / Levy, C.W. / Prince, S.M.
Citation
Journal: Biophys.J. / Year: 2020
Title: The Dual PDZ Domain from Postsynaptic Density Protein 95 Forms a Scaffold with Peptide Ligand.
Authors: Rodzli, N.A. / Lockhart-Cairns, M.P. / Levy, C.W. / Chipperfield, J. / Bird, L. / Baldock, C. / Prince, S.M.
#1: Journal: Biorxiv / Year: 2019
Title: How the dual PDZ domain from Postsynaptic density protein 95 clusters ion channels and receptors.
Authors: Rodzli, N. / Lockhart-Cairns, M.P. / Levy, C.W. / Chipperfield, J. / Bird, L. / Baldock, C. / Prince, S.M.
History
DepositionSep 2, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 2, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 22, 2020Group: Database references / Category: citation / citation_author
Revision 1.2Aug 19, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model
Item: _citation.journal_id_ISSN / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,1762
Polymers20,8691
Non-polymers3071
Water72140
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS, conformation dependent oligomer present at higher concentrations
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area350 Å2
ΔGint-3 kcal/mol
Surface area11130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.380, 50.380, 178.270
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number80
Space group name H-MI41
Components on special symmetry positions
IDModelComponents
11A-436-

HOH

21A-439-

HOH

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Components

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


Mass: 20868.662 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DLG4, PSD95 / Plasmid: pOPINF / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P78352
#2: Chemical ChemComp-GSH / GLUTATHIONE


Mass: 307.323 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N3O6S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 40 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.73 Å3/Da / Density % sol: 54.86 % / Description: Bi-pyramid
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2 M calcium acetate; 0.1 M sodium cacodylate; 40% v/v PEG 400

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.92 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jul 15, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2.04→48.48 Å / Num. obs: 14015 / % possible obs: 99.4 % / Redundancy: 11.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.05 / Net I/σ(I): 24.4
Reflection shellResolution: 2.04→2.09 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.547 / Mean I/σ(I) obs: 2.8 / Num. unique obs: 5594 / CC1/2: 0.851 / % possible all: 97.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0073 2014/05/25refinement
xia2data reduction
XDSdata reduction
SCALAdata scaling
pointlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3rl7, 3rl8

3rl7

3rl8


Resolution: 2.04→48.48 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.932 / WRfactor Rfree: 0.28 / WRfactor Rwork: 0.237 / SU B: 14.136 / SU ML: 0.206 / Cross valid method: FREE R-VALUE / ESU R: 0.219 / ESU R Free: 0.185
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2597 735 -
Rwork0.2244 13259 -
all0.226 --
obs-13994 99.389 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso mean: 65.303 Å2
Baniso -1Baniso -2Baniso -3
1--0.256 Å20 Å2-0 Å2
2---0.256 Å2-0 Å2
3---0.513 Å2
Refinement stepCycle: LAST / Resolution: 2.04→48.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1416 0 20 40 1476
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0191540
X-RAY DIFFRACTIONr_angle_refined_deg0.9961.9932080
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2235204
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.3272562
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.50715273
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.216158
X-RAY DIFFRACTIONr_chiral_restr0.0640.2233
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0211157
X-RAY DIFFRACTIONr_nbd_refined0.1790.2527
X-RAY DIFFRACTIONr_nbtor_refined0.2940.2955
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.10.247
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1660.239
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1320.25
X-RAY DIFFRACTIONr_mcbond_it1.4362.751798
X-RAY DIFFRACTIONr_mcangle_it2.5654.109999
X-RAY DIFFRACTIONr_scbond_it1.7523.125742
X-RAY DIFFRACTIONr_scangle_it2.8894.581078
X-RAY DIFFRACTIONr_lrange_it7.10723.3012007
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)WRfactor Rwork
2.04-2.0930.319430.277977104797.42120.242
2.093-2.150.282590.26490699197.37640.235
2.15-2.2120.251580.248936100399.10270.21
2.212-2.280.302500.25788593699.89320.218
2.28-2.3550.277320.25389793199.78520.213
2.355-2.4370.341340.2618538871000.222
2.437-2.5290.298390.26784588699.77430.227
2.529-2.6320.295530.27577083498.68110.239
2.632-2.7490.282340.277577911000.242
2.749-2.8820.368400.27472676799.86960.259
2.882-3.0380.373430.25666170599.85820.247
3.038-3.2210.305420.266657071000.261
3.221-3.4430.258320.2536106421000.261
3.443-3.7170.209390.2156460499.83440.223
3.717-4.0690.277290.252155299.63770.225
4.069-4.5460.182390.1714705091000.208
4.546-5.2410.247280.1554094371000.192
5.241-6.40.195100.2193773871000.259
6.4-8.9740.259150.20127228899.65280.252
8.974-48.480.234160.22115717598.85710.274
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)
12.9983-0.1990.41354.29410.19157.04350.3869-0.16520.1446-0.30130.3830.0621-0.9537-0.8731-0.76990.26390.11350.15130.43170.19530.135514.94233.795-0.083
22.51930.27680.26255.7973-5.22259.0799-0.0076-0.1107-0.16890.4381.01840.7508-0.1631-0.8872-1.01080.20710.0590.03780.73630.36960.2310.2511.27124.461
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionLabel asym-IDLabel seq-ID
1X-RAY DIFFRACTION1ALLA62 - 150
2X-RAY DIFFRACTION2ALLA157 - 245

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