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- PDB-3k82: Crystal Structure of the third PDZ domain of PSD-95 -

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Basic information

Entry
Database: PDB / ID: 3k82
TitleCrystal Structure of the third PDZ domain of PSD-95
ComponentsDisks large homolog 4
KeywordsCELL ADHESION / alpha and beta protein / Cell junction / Cell membrane / Lipoprotein / Membrane / Palmitate / Phosphoprotein / Postsynaptic cell membrane / SH3 domain / Synapse
Function / homology
Function and homology information


LGI-ADAM interactions / P2Y1 nucleotide receptor binding / beta-1 adrenergic receptor binding / neuroligin family protein binding / regulation of grooming behavior / NrCAM interactions / synaptic vesicle maturation / positive regulation of neuron projection arborization / receptor localization to synapse / vocalization behavior ...LGI-ADAM interactions / P2Y1 nucleotide receptor binding / beta-1 adrenergic receptor binding / neuroligin family protein binding / regulation of grooming behavior / NrCAM interactions / synaptic vesicle maturation / positive regulation of neuron projection arborization / receptor localization to synapse / vocalization behavior / cellular response to potassium ion / cerebellar mossy fiber / neuron spine / Synaptic adhesion-like molecules / AMPA glutamate receptor clustering / protein localization to synapse / establishment or maintenance of epithelial cell apical/basal polarity / 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 / Unblocking of NMDA receptors, glutamate binding and activation / locomotory exploration behavior / AMPA glutamate receptor complex / Long-term potentiation / Signaling by ERBB4 / neuromuscular process controlling balance / excitatory synapse / social behavior / 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 / adherens junction / PDZ domain binding / establishment of protein localization / synaptic membrane / regulation of long-term neuronal synaptic plasticity / cell-cell adhesion / postsynaptic density membrane / neuromuscular junction / 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 kinase binding / protein-containing complex 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
PHOSPHATE ION / Disks large homolog 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.4 Å
AuthorsCamara-Artigas, A. / Gavira, J.A.
CitationJournal: J.Struct.Biol. / Year: 2010
Title: Novel conformational aspects of the third PDZ domain of the neuronal post-synaptic density-95 protein revealed from two 1.4A X-ray structures
Authors: Camara-Artigas, A. / Murciano-Calles, J. / Gavira, J.A. / Cobos, E.S. / Martinez, J.C.
History
DepositionOct 13, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 7, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 12, 2014Group: Database references
Revision 1.3Apr 27, 2016Group: Other
Revision 1.4Nov 10, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / pdbx_validate_torsion / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_label_atom_id
Revision 2.1Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Disks large homolog 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,9384
Polymers10,5131
Non-polymers4253
Water1,51384
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.980, 42.980, 46.895
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number78
Space group name H-MP43

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Components

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


Mass: 10512.738 Da / Num. of mol.: 1 / Fragment: Third PDZ domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pBAT4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P78352
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 84 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.06 Å3/Da / Density % sol: 40.29 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M HEPES sodium pH 7.5, 0.8M sodium phosphate monobasic monohydrate, 0.8M potassium phosphate monobasic, VAPOR DIFFUSION, HANGING DROP, temperature 288K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.54 Å
DetectorType: Bruker Platinum 135 / Detector: CCD / Date: May 30, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.4→42.993 Å / Num. all: 16937 / Num. obs: 16934 / % possible obs: 99.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 6.7 % / Biso Wilson estimate: 13.076 Å2 / Rmerge(I) obs: 0.0548 / Rsym value: 0.0548 / Net I/σ(I): 17.5
Reflection shellResolution: 1.4→1.5 Å / Redundancy: 3.55 % / Rmerge(I) obs: 0.3079 / Mean I/σ(I) obs: 1.5 / Num. unique all: 3139 / Rsym value: 0.3079 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation1.59 Å42.98 Å
Translation1.59 Å42.98 Å

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Processing

Software
NameVersionClassificationNB
SAINTdata scaling
SCALAdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.005data extraction
PROTEUM PLUSPLUSdata collection
SAINTdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BFE

1bfe


Resolution: 1.4→20 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.952 / WRfactor Rfree: 0.224 / WRfactor Rwork: 0.175 / Occupancy max: 1 / Occupancy min: 0.1 / FOM work R set: 0.875 / SU B: 1.026 / SU ML: 0.042 / SU R Cruickshank DPI: 0.064 / SU Rfree: 0.07 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.064 / ESU R Free: 0.07 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.21 855 5.1 %RANDOM
Rwork0.172 ---
all0.174 16903 --
obs0.174 16903 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 72.48 Å2 / Biso mean: 17.095 Å2 / Biso min: 3.96 Å2
Baniso -1Baniso -2Baniso -3
1-0.28 Å20 Å20 Å2
2--0.28 Å20 Å2
3----0.56 Å2
Refinement stepCycle: LAST / Resolution: 1.4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms741 0 26 84 851
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.022795
X-RAY DIFFRACTIONr_angle_refined_deg2.0412.0031074
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1555103
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.95623.88936
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.87915131
X-RAY DIFFRACTIONr_dihedral_angle_4_deg7.543157
X-RAY DIFFRACTIONr_chiral_restr0.1350.2118
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.021587
X-RAY DIFFRACTIONr_mcbond_it1.9111.5486
X-RAY DIFFRACTIONr_mcangle_it3.0912780
X-RAY DIFFRACTIONr_scbond_it4.2963309
X-RAY DIFFRACTIONr_scangle_it6.5264.5290
LS refinement shellResolution: 1.4→1.436 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.263 68 -
Rwork0.248 1174 -
all-1242 -
obs-1174 99.92 %

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