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- PDB-1jxo: Crystal Structure of the SH3-HOOK-GK Fragment of PSD-95 -

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Basic information

Entry
Database: PDB / ID: 1jxo
TitleCrystal Structure of the SH3-HOOK-GK Fragment of PSD-95
Componentspostsynaptic density protein
KeywordsSTRUCTURAL PROTEIN / MAGUK / postsynaptic density / SH3 domain / guanylate kinase domain
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
Guanylate Kinase phosphate binding domain / Guanylate Kinase phosphate binding 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 phosphate binding domain / Guanylate Kinase phosphate binding 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. / SH3 Domains / 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 type barrels. / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Roll / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Disks large homolog 4
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsTavares, G.A. / Panepucci, E.H. / Brunger, A.T.
CitationJournal: Mol.Cell / Year: 2001
Title: Structural characterization of the intramolecular interaction between the SH3 and guanylate kinase domains of PSD-95.
Authors: Tavares, G.A. / Panepucci, E.H. / Brunger, A.T.
History
DepositionSep 7, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 16, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_sheet
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_sheet.number_strands

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: postsynaptic density protein
B: postsynaptic density protein


Theoretical massNumber of molelcules
Total (without water)69,6262
Polymers69,6262
Non-polymers00
Water3,387188
1
A: postsynaptic density protein


Theoretical massNumber of molelcules
Total (without water)34,8131
Polymers34,8131
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: postsynaptic density protein


Theoretical massNumber of molelcules
Total (without water)34,8131
Polymers34,8131
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.009, 53.410, 63.262
Angle α, β, γ (deg.)89.96, 90.00, 91.78
Int Tables number1
Space group name H-MP1

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Components

#1: Protein postsynaptic density protein / POSTSYNAPTIC DENSITY-95 / PSD-95


Mass: 34812.996 Da / Num. of mol.: 2 / Fragment: SH3-HOOK-GK
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: PSD-95 / Organ: brain / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3* / References: UniProt: P31016
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 188 / 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: 2.18 Å3/Da / Density % sol: 43.64 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.3
Details: 2-methyl-2,4-pentanediol, MES buffer, pH 6.3, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
18 mg/mlprotein1drop
25 mMGMP1drop
3100 mMMES1reservoirpH6.3
460 %MPD1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.964818 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: May 19, 2001
Details: Flat mirror (vertical focusing); single crystal Si(111) bent monochromator (horizontal focusing)
RadiationMonochromator: Flat mirror (vertical focusing); single crystal Si(111) bent monochromator (horizontal focusing)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.964818 Å / Relative weight: 1
ReflectionResolution: 2.3→29.88 Å / Num. all: 25724 / Num. obs: 25456 / % possible obs: 97.3 % / Observed criterion σ(F): 0 / Redundancy: 3 % / Biso Wilson estimate: 20 Å2 / Rsym value: 0.043
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 3 % / Num. unique all: 1270 / Rsym value: 0.106 / % possible all: 97.6
Reflection
*PLUS
Num. obs: 25724 / % possible obs: 98.4 % / Rmerge(I) obs: 0.043
Reflection shell
*PLUS
% possible obs: 97.6 % / Rmerge(I) obs: 0.102

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
CNS1.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1JXM

1jxm


Resolution: 2.3→29.88 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1763834.74 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.264 2513 9.9 %RANDOM
Rwork0.22 ---
obs0.22 25456 97.3 %-
all-25456 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 38.191 Å2 / ksol: 0.335299 e/Å3
Displacement parametersBiso mean: 28.6 Å2
Baniso -1Baniso -2Baniso -3
1-5.37 Å2-0.33 Å20 Å2
2---2.78 Å20 Å2
3----2.6 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.28 Å0.15 Å
Refinement stepCycle: LAST / Resolution: 2.3→29.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4019 0 0 188 4207
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.65
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.161.5
X-RAY DIFFRACTIONc_mcangle_it1.862
X-RAY DIFFRACTIONc_scbond_it1.82
X-RAY DIFFRACTIONc_scangle_it2.62.5
LS refinement shellResolution: 2.3→2.38 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.298 222 8.9 %
Rwork0.222 2267 -
obs--95.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
Software
*PLUS
Name: CNS / Version: 1.1 / Classification: refinement
Refinement
*PLUS
% reflection Rfree: 9.9 % / Rfactor obs: 0.22 / Rfactor Rwork: 0.22
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 28.6 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.7
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.65
X-RAY DIFFRACTIONc_mcbond_it1.161.5
X-RAY DIFFRACTIONc_scbond_it1.82
X-RAY DIFFRACTIONc_mcangle_it1.862
X-RAY DIFFRACTIONc_scangle_it2.62.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.298 / % reflection Rfree: 8.9 % / Rfactor Rwork: 0.222

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