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- PDB-5ypr: Crystal Structure of PSD-95 SH3-GK domain in complex with a synth... -

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Basic information

Entry
Database: PDB / ID: 5ypr
TitleCrystal Structure of PSD-95 SH3-GK domain in complex with a synthesized inhibitor
Components
  • Disks large homolog 4
  • Synthesized GK inhibitor
KeywordsPROTEIN BINDING / GK MAGUK inhibitor designed peptide
Function / homology
Function and homology information


RHO GTPases activate CIT / neuronal ion channel clustering / positive regulation of AMPA glutamate receptor clustering / P2Y1 nucleotide receptor binding / Neurexins and neuroligins / beta-1 adrenergic receptor binding / neuroligin family protein binding / regulation of grooming behavior / structural constituent of postsynaptic density / synaptic vesicle maturation ...RHO GTPases activate CIT / neuronal ion channel clustering / positive regulation of AMPA glutamate receptor clustering / P2Y1 nucleotide receptor binding / Neurexins and neuroligins / beta-1 adrenergic receptor binding / neuroligin family protein binding / regulation of grooming behavior / structural constituent of postsynaptic density / synaptic vesicle maturation / positive regulation of neuron projection arborization / receptor localization to synapse / dendritic spine morphogenesis / protein localization to synapse / LGI-ADAM interactions / neuron spine / cerebellar mossy fiber / Trafficking of AMPA receptors / proximal dendrite / neuromuscular process controlling balance / negative regulation of receptor internalization / vocalization behavior / Activation of Ca-permeable Kainate Receptor / juxtaparanode region of axon / positive regulation of synapse assembly / dendritic branch / positive regulation of dendrite morphogenesis / acetylcholine receptor binding / cellular response to potassium ion / frizzled binding / dendritic spine organization / RAF/MAP kinase cascade / NMDA selective glutamate receptor signaling pathway / regulation of NMDA receptor activity / beta-2 adrenergic receptor binding / Synaptic adhesion-like molecules / neurotransmitter receptor localization to postsynaptic specialization membrane / neuron projection terminus / locomotory exploration behavior / cortical cytoskeleton / AMPA glutamate receptor clustering / regulation of neuronal synaptic plasticity / social behavior / AMPA glutamate receptor complex / Unblocking of NMDA receptors, glutamate binding and activation / glutamate receptor binding / kinesin binding / D1 dopamine receptor binding / regulation of postsynaptic membrane neurotransmitter receptor levels / positive regulation of synaptic transmission / regulation of long-term neuronal synaptic plasticity / ionotropic glutamate receptor binding / excitatory synapse / dendrite cytoplasm / positive regulation of excitatory postsynaptic potential / cell periphery / synaptic membrane / establishment of protein localization / neuromuscular junction / PDZ domain binding / cell-cell adhesion / cerebral cortex development / cell junction / postsynaptic density membrane / kinase binding / cell-cell junction / nervous system development / synaptic vesicle / presynapse / positive regulation of cytosolic calcium ion concentration / protein-containing complex assembly / chemical synaptic transmission / scaffold protein binding / protein phosphatase binding / dendritic spine / postsynapse / postsynaptic membrane / neuron projection / postsynaptic density / signaling receptor binding / dendrite / protein kinase binding / synapse / protein-containing complex 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 / SH3 type barrels. / Src homology 3 domains / 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)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.349 Å
AuthorsZhu, J. / Zhou, Q. / Shang, Y. / Weng, Z. / Zhu, R. / Zhang, M.
Funding support China, Hong Kong, 4items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)31770779, 31470733 and U1532121 China
Shanghai Municipal Science and Technology Commission14YF1406700 China
RGC16103614, 16149516 and AoE-M09-12 Hong Kong
the Minister of Science and Technology of China2014CB910204 China
CitationJournal: Cell Rep / Year: 2017
Title: Synaptic Targeting and Function of SAPAPs Mediated by Phosphorylation-Dependent Binding to PSD-95 MAGUKs.
Authors: Zhu, J. / Zhou, Q. / Shang, Y. / Li, H. / Peng, M. / Ke, X. / Weng, Z. / Zhang, R. / Huang, X. / Li, S.S.C. / Feng, G. / Lu, Y. / Zhang, M.
History
DepositionNov 2, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 14, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 23, 2022Group: Author supporting evidence / Database references / Category: database_2 / pdbx_audit_support
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization
Revision 1.2Nov 22, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Oct 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
B: Synthesized GK inhibitor


Theoretical massNumber of molelcules
Total (without water)38,8922
Polymers38,8922
Non-polymers00
Water75742
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1730 Å2
ΔGint-4 kcal/mol
Surface area14660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.028, 45.743, 86.358
Angle α, β, γ (deg.)90.00, 103.22, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-819-

HOH

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Components

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


Mass: 36835.223 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Dlg4, Dlgh4, Psd95 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P31016
#2: Protein/peptide Synthesized GK inhibitor


Mass: 2056.314 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 42 / 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: 2.94 Å3/Da / Density % sol: 58.2 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 8 / Details: 0.1M tris pH 8.0, 35% tert-Butanol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 12, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 2.349→50 Å / Num. obs: 19033 / % possible obs: 99.2 % / Redundancy: 5.8 % / Net I/σ(I): 16.3

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1KJW

1kjw


Resolution: 2.349→38.46 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2637 974 5.14 %
Rwork0.2215 --
obs0.2237 18966 98.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.349→38.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2215 0 0 42 2257
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032264
X-RAY DIFFRACTIONf_angle_d0.6333062
X-RAY DIFFRACTIONf_dihedral_angle_d13.209811
X-RAY DIFFRACTIONf_chiral_restr0.025332
X-RAY DIFFRACTIONf_plane_restr0.002402
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3487-2.47250.32581440.28062505X-RAY DIFFRACTION98
2.4725-2.62740.32171540.27432567X-RAY DIFFRACTION99
2.6274-2.83020.34721170.26112543X-RAY DIFFRACTION98
2.8302-3.11490.27741300.25982580X-RAY DIFFRACTION99
3.1149-3.56530.25931440.23842582X-RAY DIFFRACTION99
3.5653-4.49080.25041430.20032579X-RAY DIFFRACTION99
4.4908-38.46560.23961420.19492636X-RAY DIFFRACTION98

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