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- PDB-5ypo: Crystal structure of PSD-95 GK domain in complex with phospho-SAP... -

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Basic information

Entry
Database: PDB / ID: 5ypo
TitleCrystal structure of PSD-95 GK domain in complex with phospho-SAPAP peptide
Components
  • Disks large homolog 4
  • SAPAP
KeywordsPROTEIN BINDING / PSD-95 SAPAP phosphorylation Synapse
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 / postsynaptic specialization ...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 / postsynaptic specialization / synaptic vesicle maturation / positive regulation of neuron projection arborization / receptor localization to synapse / protein localization to synapse / cerebellar mossy fiber / dendritic spine morphogenesis / LGI-ADAM interactions / neuron spine / Trafficking of AMPA receptors / proximal dendrite / negative regulation of receptor internalization / vocalization behavior / juxtaparanode region of axon / Activation of Ca-permeable Kainate Receptor / dendritic branch / positive regulation of synapse assembly / neuromuscular process controlling balance / positive regulation of dendrite morphogenesis / acetylcholine receptor binding / frizzled binding / cellular response to potassium ion / dendritic spine organization / regulation of NMDA receptor activity / RAF/MAP kinase cascade / NMDA selective glutamate receptor signaling pathway / beta-2 adrenergic receptor binding / Synaptic adhesion-like molecules / Neurexins and neuroligins / neurotransmitter receptor localization to postsynaptic specialization membrane / neuron projection terminus / cortical cytoskeleton / AMPA glutamate receptor clustering / locomotory exploration behavior / social behavior / regulation of neuronal synaptic plasticity / AMPA glutamate receptor complex / Unblocking of NMDA receptors, glutamate binding and activation / glutamate receptor binding / kinesin binding / D1 dopamine receptor binding / positive regulation of synaptic transmission / regulation of postsynaptic membrane neurotransmitter receptor levels / ionotropic glutamate receptor binding / dendrite cytoplasm / excitatory synapse / positive regulation of excitatory postsynaptic potential / cell periphery / synaptic membrane / PDZ domain binding / neuromuscular junction / establishment of protein localization / regulation of long-term neuronal synaptic plasticity / cell-cell adhesion / cerebral cortex development / cell junction / postsynaptic density membrane / modulation of chemical synaptic transmission / kinase binding / cell-cell junction / nervous system development / synaptic vesicle / positive regulation of cytosolic calcium ion concentration / protein-containing complex assembly / scaffold protein binding / chemical synaptic transmission / protein phosphatase binding / molecular adaptor activity / dendritic spine / postsynaptic membrane / postsynapse / postsynaptic density / neuron projection / signaling receptor binding / synapse / dendrite / protein kinase binding / protein-containing complex binding / glutamatergic synapse / endoplasmic reticulum / membrane / plasma membrane / cytosol / cytoplasm
Similarity search - Function
SAPAP family / Guanylate-kinase-associated protein (GKAP) protein / 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 ...SAPAP family / Guanylate-kinase-associated protein (GKAP) protein / 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 / 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 / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Disks large-associated protein 1 / Disks large homolog 4
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.29 Å
AuthorsZhu, J. / Zhou, Q. / Shang, Y. / Weng, Z. / Zhang, R. / Zhang, M.
Funding support China, Hong Kong, 8items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)31770779 China
National Science Foundation (NSF, United States)31470733 China
National Science Foundation (NSF, United States)U1532121 China
Shanghai Municipal Science and Technology Commission14YF1406700 China
the Minister of Science and Technology of China2014CB910204 China
RGC16103614 Hong Kong
RGC16149516 Hong Kong
RGCAoE-M09-12 Hong Kong
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 1.3Nov 20, 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
B: Disks large homolog 4
A: Disks large homolog 4
C: SAPAP
D: SAPAP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,2057
Polymers46,9294
Non-polymers2763
Water3,729207
1
B: Disks large homolog 4
C: SAPAP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,6494
Polymers23,4642
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1670 Å2
ΔGint-7 kcal/mol
Surface area10670 Å2
MethodPISA
2
A: Disks large homolog 4
D: SAPAP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,5563
Polymers23,4642
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1470 Å2
ΔGint-5 kcal/mol
Surface area10340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)33.776, 84.063, 165.123
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 21690.418 Da / Num. of mol.: 2
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 SAPAP


Mass: 1773.901 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: O14490*PLUS
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 207 / 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: 2.5 Å3/Da / Density % sol: 50.75 %
Crystal growTemperature: 289 K / Method: vapor diffusion / pH: 5.5
Details: Condition: 0.1 M Ammonium acetate, 0.1 M BIS-TRIS pH 5.5, 17% w/v Polyethylene glycol 10000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 22, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.29→50 Å / Num. obs: 21711 / % possible obs: 99.1 % / Redundancy: 6.5 % / Net I/σ(I): 17.1
Reflection shellResolution: 2.35→2.39 Å

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3UAT

3uat


Resolution: 2.29→37.457 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2257 1116 5.15 %
Rwork0.1791 --
obs0.1815 21665 98.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.29→37.457 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3110 0 18 207 3335
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083215
X-RAY DIFFRACTIONf_angle_d0.8624348
X-RAY DIFFRACTIONf_dihedral_angle_d9.7832653
X-RAY DIFFRACTIONf_chiral_restr0.054476
X-RAY DIFFRACTIONf_plane_restr0.006572
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2896-2.39380.27771240.1982333X-RAY DIFFRACTION91
2.3938-2.520.22371580.18812536X-RAY DIFFRACTION100
2.52-2.67790.26771420.20112561X-RAY DIFFRACTION100
2.6779-2.88460.27561240.19462589X-RAY DIFFRACTION100
2.8846-3.17470.23231290.19592607X-RAY DIFFRACTION100
3.1747-3.63380.23831460.1752599X-RAY DIFFRACTION99
3.6338-4.57690.20571420.1582611X-RAY DIFFRACTION99
4.5769-37.46190.19071510.17212713X-RAY DIFFRACTION97

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