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- PDB-3gsl: Crystal structure of PSD-95 tandem PDZ domains 1 and 2 -

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Basic information

Entry
Database: PDB / ID: 3gsl
TitleCrystal structure of PSD-95 tandem PDZ domains 1 and 2
ComponentsDisks large homolog 4
KeywordsSTRUCTURAL PROTEIN / PDZ domain / tandem / PSD-95 / DLG4 / SAP-90 / GluR6 / Cell junction / Cell membrane / Lipoprotein / Membrane / Palmitate / Phosphoprotein / Postsynaptic cell membrane / SH3 domain / Synapse
Function / homology
Function and homology information


RHO GTPases activate CIT / positive regulation of AMPA glutamate receptor clustering / neuronal ion channel clustering / P2Y1 nucleotide receptor binding / Neurexins and neuroligins / beta-1 adrenergic receptor binding / neuroligin family protein binding / structural constituent of postsynaptic density / proximal dendrite / receptor localization to synapse ...RHO GTPases activate CIT / positive regulation of AMPA glutamate receptor clustering / neuronal ion channel clustering / P2Y1 nucleotide receptor binding / Neurexins and neuroligins / beta-1 adrenergic receptor binding / neuroligin family protein binding / structural constituent of postsynaptic density / proximal dendrite / receptor localization to synapse / positive regulation of neuron projection arborization / regulation of grooming behavior / synaptic vesicle maturation / cerebellar mossy fiber / cellular response to potassium ion / protein localization to synapse / vocalization behavior / LGI-ADAM interactions / Trafficking of AMPA receptors / neuron spine / dendritic branch / Activation of Ca-permeable Kainate Receptor / AMPA glutamate receptor clustering / juxtaparanode region of axon / establishment or maintenance of epithelial cell apical/basal polarity / dendritic spine morphogenesis / frizzled binding / negative regulation of receptor internalization / postsynaptic neurotransmitter receptor diffusion trapping / neuron projection terminus / dendritic spine organization / acetylcholine receptor binding / positive regulation of synapse assembly / RAF/MAP kinase cascade / Synaptic adhesion-like molecules / neurotransmitter receptor localization to postsynaptic specialization membrane / positive regulation of dendrite morphogenesis / beta-2 adrenergic receptor binding / cortical cytoskeleton / regulation of neuronal synaptic plasticity / locomotory exploration behavior / regulation of NMDA receptor activity / social behavior / positive regulation of excitatory postsynaptic potential / kinesin binding / AMPA glutamate receptor complex / neuromuscular process controlling balance / excitatory synapse / D1 dopamine receptor binding / Unblocking of NMDA receptors, glutamate binding and activation / glutamate 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 / synaptic membrane / PDZ domain binding / cell periphery / postsynaptic density membrane / regulation of long-term neuronal synaptic plasticity / neuromuscular junction / establishment of protein localization / cell-cell adhesion / cerebral cortex development / kinase binding / cell-cell junction / synaptic vesicle / cell junction / positive regulation of cytosolic calcium ion concentration / chemical synaptic transmission / postsynapse / scaffold protein binding / postsynaptic membrane / basolateral plasma membrane / protein phosphatase binding / protein-containing complex assembly / dendritic spine / postsynaptic density / neuron projection / signaling receptor binding / dendrite / synapse / glutamatergic synapse / protein-containing complex binding / protein kinase binding / endoplasmic reticulum / membrane / 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 / 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
Disks large homolog 4
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsSainlos, M. / Olivier, N.B. / Imperiali, B.
CitationJournal: Nat.Chem.Biol. / Year: 2011
Title: Biomimetic divalent ligands for the acute disruption of synaptic AMPAR stabilization.
Authors: Sainlos, M. / Tigaret, C. / Poujol, C. / Olivier, N.B. / Bard, L. / Breillat, C. / Thiolon, K. / Choquet, D. / Imperiali, B.
History
DepositionMar 27, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 29, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: 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_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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)41,5812
Polymers41,5812
Non-polymers00
Water5,044280
1
A: Disks large homolog 4


Theoretical massNumber of molelcules
Total (without water)20,7911
Polymers20,7911
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Disks large homolog 4


Theoretical massNumber of molelcules
Total (without water)20,7911
Polymers20,7911
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.244, 62.511, 59.342
Angle α, β, γ (deg.)90.00, 99.25, 90.00
Int Tables number4
Space group name H-MP1211
DetailsAUTHORS STATE THAT ONE PROTOMER OF THE ASYMMETRIC UNIT IS THE BIOLOGICAL ASSEMBLY.

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Components

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


Mass: 20790.654 Da / Num. of mol.: 2 / Fragment: PDZ domains 1 and 2: UNP residues 61-249
Source method: isolated from a genetically manipulated source
Details: N-terminal, TEV cleavable octahistidine tag. Three N-terminal residues S-G-S remain after proteolysis.
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Dlg4, Dlgh4, PSD-95, Psd95 / Plasmid: pET-NO / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P31016
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 280 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsPDZ DOMAIN 1 LIGAND (ETMA) IS FUSED TO THE C-TERMINUS OF DOMAIN 2.

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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: 2.48 Å3/Da / Density % sol: 50.36 %
Description: THE ENTRY HAS BEEN UPDATED WITH THE COORDINATES OBTAINED FROM REFINEMENT USING DATA COLLECTED ON 2009-06-26
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 35% v/v 2-methyl-2,4-pentanediol, 0.1M Tris-HCl pH 7.0. 0.2M NaCl, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 0.97 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Feb 6, 2009 / Details: Toroidal focusing mirror
RadiationMonochromator: Si(111) channel cut / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.05→50 Å / Num. all: 26112 / Num. obs: 25616 / % possible obs: 98.1 % / Redundancy: 3.7 % / Biso Wilson estimate: 35.16 Å2 / Rmerge(I) obs: 0.058 / Net I/σ(I): 21.2
Reflection shellResolution: 2.05→2.12 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.349 / Mean I/σ(I) obs: 3.1 / Num. unique all: 2594 / % possible all: 96.3

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
REFMAC5.1.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entries 2I1N, 2FE5

2i1n

2fe5


Resolution: 2.05→32.31 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.909 / Cross valid method: THROUGHOUT / ESU R: 0.251 / ESU R Free: 0.222 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28146 2576 10.1 %RANDOM
Rwork0.21412 ---
obs0.2209 25598 98.09 %-
all-25616 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.914 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å20 Å20.07 Å2
2---1.18 Å20 Å2
3---1.24 Å2
Refinement stepCycle: LAST / Resolution: 2.05→32.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2864 0 0 280 3144
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0222905
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.6311.9743930
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.945385
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.67424.957117
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.01515497
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.2121516
X-RAY DIFFRACTIONr_chiral_restr0.0540.2455
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.022176
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2750.21349
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3280.22012
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1960.2280
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3310.252
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2340.219
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.6311.51907
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.82723053
X-RAY DIFFRACTIONr_scbond_it5.9243998
X-RAY DIFFRACTIONr_scangle_it8.4654.5877
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.05→2.103 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.341 174 -
Rwork0.259 1659 -
obs--96.42 %

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