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- PDB-6spz: Crystal structure of PDZ1-2 from PSD-95 with peptide ligand seque... -

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Basic information

Entry
Database: PDB / ID: 6spz
TitleCrystal structure of PDZ1-2 from PSD-95 with peptide ligand sequence RRESEI bound to both domains
Components
  • ARG-ARG-GLU-SER-GLU-ILE
  • Disks large homolog 4
KeywordsSTRUCTURAL PROTEIN / PSD-95 fragment / clustering / protein-complex / receptor-binding / membrane associated
Function / homology
Function and homology information


Sensory perception of sour taste / Classical Kir channels / regulation of skeletal muscle contraction via regulation of action potential / relaxation of skeletal muscle / LGI-ADAM interactions / Phase 4 - resting membrane potential / magnesium ion transport / voltage-gated potassium channel activity involved in cardiac muscle cell action potential repolarization / membrane repolarization during action potential / P2Y1 nucleotide receptor binding ...Sensory perception of sour taste / Classical Kir channels / regulation of skeletal muscle contraction via regulation of action potential / relaxation of skeletal muscle / LGI-ADAM interactions / Phase 4 - resting membrane potential / magnesium ion transport / voltage-gated potassium channel activity involved in cardiac muscle cell action potential repolarization / membrane repolarization during action potential / P2Y1 nucleotide receptor binding / beta-1 adrenergic receptor binding / neuroligin family protein binding / NrCAM interactions / membrane repolarization during cardiac muscle cell action potential / regulation of resting membrane potential / 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 / regulation of membrane repolarization / cerebellar mossy fiber / Synaptic adhesion-like molecules / protein localization to synapse / vocalization behavior / intracellular potassium ion homeostasis / positive regulation of potassium ion transmembrane transport / neuron spine / membrane depolarization during cardiac muscle cell action potential / inward rectifier potassium channel activity / cardiac muscle cell action potential involved in contraction / juxtaparanode region of axon / neuron projection terminus / regulation of cardiac muscle cell contraction / 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 / regulation of monoatomic ion transmembrane transport / acetylcholine receptor binding / Neurexins and neuroligins / neurotransmitter receptor localization to postsynaptic specialization membrane / Activation of Ca-permeable Kainate Receptor / relaxation of cardiac muscle / locomotory exploration behavior / cortical cytoskeleton / potassium ion import across plasma membrane / Signaling by ERBB4 / Negative regulation of NMDA receptor-mediated neuronal transmission / Unblocking of NMDA receptors, glutamate binding and activation / regulation of heart rate by cardiac conduction / smooth endoplasmic reticulum / 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 / intercalated disc / positive regulation of protein tyrosine kinase activity / rough endoplasmic reticulum / voltage-gated potassium channel complex / positive regulation of synaptic transmission / potassium ion transmembrane transport / ionotropic glutamate receptor binding / phosphatidylinositol-4,5-bisphosphate binding / T-tubule / 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 / Activation of G protein gated Potassium channels / Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits / potassium ion transport / cell-cell adhesion / kinase binding / cellular response to mechanical stimulus / 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 / protein homotetramerization
Similarity search - Function
Potassium channel, inwardly rectifying, Kir2.1 / Potassium channel, inwardly rectifying, Kir, N-terminal / Inward rectifier potassium channel N-terminal / 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 / Potassium channel, inwardly rectifying, transmembrane domain ...Potassium channel, inwardly rectifying, Kir2.1 / Potassium channel, inwardly rectifying, Kir, N-terminal / Inward rectifier potassium channel N-terminal / 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 / Potassium channel, inwardly rectifying, transmembrane domain / Inward rectifier potassium channel transmembrane domain / Potassium channel, inwardly rectifying, Kir, cytoplasmic / Potassium channel, inwardly rectifying, Kir / Inward rectifier potassium channel, C-terminal / Inward rectifier potassium channel C-terminal domain / 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 / Immunoglobulin E-set / Roll / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
GLUTATHIONE / Inward rectifier potassium channel 2 / Disks large homolog 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.08 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 3, 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
P: ARG-ARG-GLU-SER-GLU-ILE
Q: ARG-ARG-GLU-SER-GLU-ILE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,7584
Polymers22,4503
Non-polymers3071
Water1,00956
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS, oligomers formed at high concentration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2220 Å2
ΔGint-10 kcal/mol
Surface area11570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.500, 50.500, 176.370
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number80
Space group name H-MI41
Noncrystallographic symmetry (NCS)NCS domain: (Details: Chains P Q)

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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 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P78352
#2: Protein/peptide ARG-ARG-GLU-SER-GLU-ILE


Mass: 790.866 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Syntheic peptide / Source: (synth.) Homo sapiens (human) / References: UniProt: P63252*PLUS
#3: Chemical ChemComp-GSH / GLUTATHIONE / Glutathione


Mass: 307.323 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C10H17N3O6S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 56 / 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: 2.58 Å3/Da / Density % sol: 52.41 % / Description: tetragonal bipyramid
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.2
Details: 0.2 M NaCl, 0.1 M Na/K phosphate, 50% v/v PEG 200. Matrix microseeding with Apo crystal form (PDB ID: 6spv).

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 15, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.08→48.55 Å / Num. obs: 13236 / % possible obs: 100 % / Redundancy: 7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.075 / Net I/σ(I): 14.5
Reflection shellResolution: 2.08→2.13 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.538 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 980 / CC1/2: 0.762 / % possible all: 99.9

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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: 2.08→48.549 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.937 / SU B: 11.386 / SU ML: 0.155 / Cross valid method: FREE R-VALUE / ESU R: 0.225 / ESU R Free: 0.185
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2399 703 -
Rwork0.2004 --
all0.203 --
obs-13216 99.97 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å
Displacement parametersBiso mean: 47.492 Å2
Baniso -1Baniso -2Baniso -3
1-0.226 Å2-0 Å2-0 Å2
2--0.226 Å2-0 Å2
3----0.451 Å2
Refinement stepCycle: LAST / Resolution: 2.08→48.549 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1526 0 20 56 1602
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0191620
X-RAY DIFFRACTIONr_angle_refined_deg1.1391.9942184
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.465206
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.26724.50771
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.13115289
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.771512
X-RAY DIFFRACTIONr_chiral_restr0.0950.2245
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0211229
X-RAY DIFFRACTIONr_nbd_refined0.190.2661
X-RAY DIFFRACTIONr_nbtor_refined0.2960.21047
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1160.245
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1850.238
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1530.29
X-RAY DIFFRACTIONr_mcbond_it1.7543.134827
X-RAY DIFFRACTIONr_mcangle_it3.0724.6671032
X-RAY DIFFRACTIONr_scbond_it1.9413.624793
X-RAY DIFFRACTIONr_scangle_it3.2535.2841152
X-RAY DIFFRACTIONr_lrange_it7.32826.4272252
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
2.08-2.1340.284540.26792097599.89740.243
2.134-2.1930.247630.2338879501000.21
2.193-2.2560.299480.2278839311000.201
2.256-2.3250.249340.2088538871000.185
2.325-2.4010.35320.2068568881000.183
2.401-2.4850.237390.2057908291000.179
2.485-2.5790.26360.2097758111000.186
2.579-2.6840.285480.2217397871000.2
2.684-2.8030.328410.2267127531000.209
2.803-2.9390.269350.21466570199.85730.204
2.939-3.0980.261430.2146326751000.211
3.098-3.2850.288320.2146196511000.219
3.285-3.510.192270.2175856121000.229
3.51-3.790.244400.18352356499.82270.196
3.79-4.1490.202350.1834925271000.207
4.149-4.6350.178350.1424354701000.168
4.635-5.3440.212210.1693934141000.206
5.344-6.5250.318110.22734435699.71910.268
6.525-9.1450.175170.1912632801000.227
9.145-48.5490.291120.2241471591000.305
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)
12.4368-0.18850.07453.5596-0.34473.51610.0004-0.09270.08690.04440.15610.2073-0.2681-0.3032-0.15650.07350.06250.04860.0890.05430.049815.00434.6210.241
21.56480.56920.0512.9813-1.20495.76710.14280.24370.1597-0.16170.09570.1856-0.0683-0.102-0.23850.04440.01060.00770.19010.13140.10449.54111.83124.127
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA61 - 15161 - 151
21PB423 - 427423 - 427
32AA158 - 244158 - 244
42QC423 - 427423 - 427

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