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- PDB-1bfe: THE THIRD PDZ DOMAIN FROM THE SYNAPTIC PROTEIN PSD-95 -

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Basic information

Entry
Database: PDB / ID: 1bfe
TitleTHE THIRD PDZ DOMAIN FROM THE SYNAPTIC PROTEIN PSD-95
ComponentsPSD-95
KeywordsPEPTIDE RECOGNITION / PROTEIN LOCALIZATION
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 / beta-1 adrenergic receptor binding / Neurexins and neuroligins / neuroligin family protein binding / structural constituent of postsynaptic density / synaptic vesicle maturation / positive regulation of neuron projection arborization ...RHO GTPases activate CIT / positive regulation of AMPA glutamate receptor clustering / neuronal ion channel clustering / P2Y1 nucleotide receptor binding / beta-1 adrenergic receptor binding / Neurexins and neuroligins / neuroligin family protein binding / structural constituent of postsynaptic density / synaptic vesicle maturation / positive regulation of neuron projection arborization / regulation of grooming behavior / receptor localization to synapse / vocalization behavior / cerebellar mossy fiber / LGI-ADAM interactions / proximal dendrite / neuron spine / Trafficking of AMPA receptors / protein localization to synapse / AMPA glutamate receptor clustering / cellular response to potassium ion / Activation of Ca-permeable Kainate Receptor / dendritic branch / positive regulation of dendrite morphogenesis / dendritic spine morphogenesis / negative regulation of receptor internalization / juxtaparanode region of axon / frizzled binding / acetylcholine receptor binding / neuron projection terminus / dendritic spine organization / regulation of NMDA receptor activity / positive regulation of synapse assembly / Synaptic adhesion-like molecules / NMDA selective glutamate receptor signaling pathway / RAF/MAP kinase cascade / beta-2 adrenergic receptor binding / neurotransmitter receptor localization to postsynaptic specialization membrane / cortical cytoskeleton / social behavior / locomotory exploration behavior / AMPA glutamate receptor complex / regulation of neuronal synaptic plasticity / neuromuscular process controlling balance / kinesin binding / excitatory synapse / positive regulation of excitatory postsynaptic potential / Unblocking of NMDA receptors, glutamate binding and activation / positive regulation of synaptic transmission / glutamate receptor binding / D1 dopamine receptor binding / regulation of postsynaptic membrane neurotransmitter receptor levels / ionotropic glutamate receptor binding / dendrite cytoplasm / cell periphery / PDZ domain binding / establishment of protein localization / regulation of long-term neuronal synaptic plasticity / synaptic membrane / postsynaptic density membrane / neuromuscular junction / cerebral cortex development / cell-cell adhesion / kinase binding / cell junction / synaptic vesicle / cell-cell junction / nervous system development / positive regulation of cytosolic calcium ion concentration / protein-containing complex assembly / scaffold protein binding / protein phosphatase binding / chemical synaptic transmission / dendritic spine / postsynaptic membrane / postsynapse / neuron projection / postsynaptic density / signaling receptor binding / synapse / dendrite / protein-containing complex binding / protein kinase binding / glutamatergic synapse / 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. ...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 / MIR / Resolution: 2.3 Å
AuthorsDoyle, D.A. / Lee, A. / Lewis, J. / Kim, E. / Sheng, M. / Mackinnon, R.
Citation
Journal: Cell(Cambridge,Mass.) / Year: 1996
Title: Crystal structures of a complexed and peptide-free membrane protein-binding domain: molecular basis of peptide recognition by PDZ.
Authors: Doyle, D.A. / Lee, A. / Lewis, J. / Kim, E. / Sheng, M. / MacKinnon, R.
#1: Journal: Nat.Struct.Biol. / Year: 1998
Title: Crystal Structure of the Hcask Pdz Domain Reveals Structural Basis of Class II Pdz Domain Target Recognition
Authors: Daniels, D.L. / Cohen, A.R. / Anderson, J.M. / Brunger, A.T.
#2: Journal: Nature / Year: 1996
Title: Crystal Structure of a Pdz Domain
Authors: Cabral, M. / Petosa, C. / Sutcliffe, M.J. / Raza, S. / Byron, O. / Poy, F. / Marfatia, S.M. / Chishti, A.H. / Liddington, R.C.
History
DepositionMay 20, 1998Processing site: BNL
Revision 1.0Oct 21, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
Revision 1.4Mar 7, 2018Group: Data collection / Other / Category: diffrn_source / pdbx_database_status
Item: _diffrn_source.source / _pdbx_database_status.process_site
Revision 1.5Feb 7, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PSD-95


Theoretical massNumber of molelcules
Total (without water)12,7501
Polymers12,7501
Non-polymers00
Water2,000111
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)89.200, 89.200, 89.200
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number213
Space group name H-MP4132
Components on special symmetry positions
IDModelComponents
11A-66-

HOH

21A-72-

HOH

31A-103-

HOH

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Components

#1: Protein PSD-95


Mass: 12750.126 Da / Num. of mol.: 1 / Fragment: THE THIRD PDZ DOMAIN OF PSD-95
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Plasmid: PGEX-4T-1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P31016
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 111 / 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: 2.32 Å3/Da / Density % sol: 46.95 %
Crystal growpH: 7.5 / Details: 0.8 M SODIUM CITRATE, 0.1 M HEPES, PH 7.5
Crystal
*PLUS
Crystal grow
*PLUS
Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
10.8 Msodium citrate1reservoir
20.1 MHEPES1reservoirpH7.5
315 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: SIEMENS / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 1, 1996 / Details: COLLIMATOR
RadiationMonochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→20 Å / Num. obs: 6421 / % possible obs: 96.6 % / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.036
Reflection shellResolution: 2.3→2.38 Å / Rmerge(I) obs: 0.166 / % possible all: 86.7
Reflection
*PLUS
Num. measured all: 38267
Reflection shell
*PLUS
% possible obs: 90.2 %

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
MOSFLMdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementMethod to determine structure: MIR / Resolution: 2.3→20 Å / Rfactor Rfree: 0.315 / Rfactor Rwork: 0.214
Refinement stepCycle: LAST / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms826 0 0 111 937
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.3 Å / Rfactor obs: 0.214 / Rfactor Rfree: 0.315 / Lowest resolution: 6 Å / σ(F): 2 / % reflection Rfree: 10 % / Num. reflection obs: 5322
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.013
X-RAY DIFFRACTIONx_angle_deg1.8

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