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- PDB-5jxb: PSD-95 extended PDZ3 in complex with SynGAP PBM -

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Basic information

Entry
Database: PDB / ID: 5jxb
TitlePSD-95 extended PDZ3 in complex with SynGAP PBM
ComponentsDisks large homolog 4,SynGAP
KeywordsCELL ADHESION / PSD-95 / PDZ / SynGAP / Extension
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 / neuron spine / Synaptic adhesion-like molecules / cerebellar mossy fiber / establishment or maintenance of epithelial cell apical/basal polarity / protein localization to synapse / Trafficking of AMPA receptors / dendritic spine morphogenesis / negative regulation of receptor internalization / juxtaparanode region of axon / acetylcholine receptor binding / RHO GTPases activate CIT / cellular response to potassium ion / Assembly and cell surface presentation of NMDA receptors / NMDA selective glutamate receptor signaling pathway / Neurexins and neuroligins / neuromuscular process controlling balance / Activation of Ca-permeable Kainate Receptor / neurotransmitter receptor localization to postsynaptic specialization membrane / cortical cytoskeleton / neuron projection terminus / Negative regulation of NMDA receptor-mediated neuronal transmission / Unblocking of NMDA receptors, glutamate binding and activation / AMPA glutamate receptor clustering / locomotory exploration behavior / Signaling by ERBB4 / AMPA glutamate receptor complex / Long-term potentiation / social behavior / D1 dopamine receptor binding / positive regulation of synaptic transmission / regulation of postsynaptic membrane neurotransmitter receptor levels / excitatory synapse / ionotropic glutamate receptor binding / dendrite cytoplasm / Ras activation upon Ca2+ influx through NMDA receptor / synaptic membrane / positive regulation of excitatory postsynaptic potential / learning / PDZ domain binding / adherens junction / neuromuscular junction / establishment of protein localization / cell-cell adhesion / regulation of long-term neuronal synaptic plasticity / postsynaptic density membrane / kinase binding / synaptic vesicle / endocytic vesicle membrane / cell junction / nervous system development / positive regulation of cytosolic calcium ion concentration / RAF/MAP kinase cascade / protein-containing complex assembly / scaffold protein binding / protein phosphatase binding / dendritic spine / chemical synaptic transmission / postsynaptic membrane / neuron projection / postsynaptic density / synapse / protein kinase binding / protein-containing complex binding / glutamatergic synapse / endoplasmic reticulum / signal transduction / plasma membrane / cytoplasm / cytosol
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 speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsShang, Y. / Zhang, M.
Funding support Hong Kong, China, 5items
OrganizationGrant numberCountry
RGC663811 Hong Kong
RGC663812 Hong Kong
RGCT13-607/12R Hong Kong
RGCAoE-M09-12 Hong Kong
the Minister of Science and Technology of China2014CB910204 China
CitationJournal: Cell / Year: 2016
Title: Phase Transition in Postsynaptic Densities Underlies Formation of Synaptic Complexes and Synaptic Plasticity.
Authors: Zeng, M. / Shang, Y. / Araki, Y. / Guo, T. / Huganir, R.L. / Zhang, M.
History
DepositionMay 13, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 28, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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 / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Disks large homolog 4,SynGAP
C: Disks large homolog 4,SynGAP


Theoretical massNumber of molelcules
Total (without water)26,8162
Polymers26,8162
Non-polymers00
Water724
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area920 Å2
ΔGint-3 kcal/mol
Surface area12660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.286, 71.094, 115.791
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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


Mass: 13407.992 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: The fusion protein of PSD-95 (PDZ3 RESIDUES 306-410), LINKER (GSGS), AND SynGAP (RESIDUES 415-426)
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Mus musculus (house mouse)
Gene: DLG4, PSD95 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P78352
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / 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: 2.49 Å3/Da / Density % sol: 50.54 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M HEPES sodium pH 7.5, 10% v/v 2-Propanol, 20% w/v Polyethylene glycol 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 22, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 6680 / % possible obs: 99.2 % / Redundancy: 7 % / Net I/σ(I): 43.3

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Processing

Software
NameVersionClassification
PHENIX1.10_2155refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BE9

1be9


Resolution: 2.9→45.89 Å / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 37.83 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2874 319 4.78 %
Rwork0.2407 --
obs0.2411 6641 99.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.9→45.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1777 0 0 4 1781
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0171809
X-RAY DIFFRACTIONf_angle_d1.8672446
X-RAY DIFFRACTIONf_dihedral_angle_d28.202650
X-RAY DIFFRACTIONf_chiral_restr0.091269
X-RAY DIFFRACTIONf_plane_restr0.012328
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9052-3.65790.3491450.29583116X-RAY DIFFRACTION95
3.6579-22.94570.2621710.21333206X-RAY DIFFRACTION94
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.087-1.6443-0.31793.6081-2.24629.1703-0.12740.4615-0.0347-0.6973-0.0470.0071.0748-0.8210.23640.9283-0.07860.06680.83830.2280.3097-5.3898-23.89728.5035
20.2604-0.11210.22150.16860.03620.33230.04570.3809-0.134-0.1866-0.18210.01370.492-0.00680.11091.5758-0.61340.10241.2052-0.07120.4108-17.043-33.462813.3843
33.92960.1134-1.41164.54122.10372.9927-0.22350.489-0.5374-0.0349-0.14060.01121.0614-0.63730.37631.3279-0.23340.14090.9815-0.05320.1759-9.4709-30.70916.3647
42.5341-0.0472-0.02873.3151-2.56714.65670.10310.30810.0183-0.0299-0.16130.0005-0.0267-0.94680.07890.8528-0.05010.09090.8085-0.05080.134-12.1309-24.313221.2068
53.19781.8646-0.01783.3535-0.5522.011-0.42650.6789-0.4437-0.35410.3571-0.00530.58560.06730.06521.1675-0.3790.52220.7932-0.25140.7152-16.4682-31.736627.4143
63.8143-3.0175-3.7385.89114.23834.1363-0.4270.02580.14730.50790.4337-0.0840.16680.7051-0.02131.35430.2197-0.06421.0717-0.02660.2207-11.7021-4.6534-19.7599
73.01460.11280.05711.3005-0.34647.27820.1827-0.1324-0.2713-0.391-0.187-0.23580.75020.68820.04311.37460.49320.00480.88710.04890.2138-4.1463-13.6862-11.2193
82.0093-0.03050.38860.51310.66153.5080.14010.0814-0.036-0.20860.07130.03530.16030.53660.00541.2937-0.0091-0.03660.75480.12220.119-10.376-10.955-15.7386
91.1992-0.08130.74490.5145-0.93313.9544-0.1703-0.0051-0.18360.0741-0.133-0.26810.96830.48320.10341.36540.16120.08450.61150.02230.2382-8.383-11.1031-5.2878
100.51540.71231.38490.98261.91293.7205-0.19890.43260.1652-0.8490.2494-0.0618-0.47710.2843-0.05931.07470.24560.03471.1725-0.02610.2988-2.5111-15.896-1.6605
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 305 through 314 )
2X-RAY DIFFRACTION2chain 'A' and (resid 315 through 325 )
3X-RAY DIFFRACTION3chain 'A' and (resid 326 through 353 )
4X-RAY DIFFRACTION4chain 'A' and (resid 354 through 410 )
5X-RAY DIFFRACTION5chain 'A' and (resid 416 through 426 )
6X-RAY DIFFRACTION6chain 'C' and (resid 304 through 314 )
7X-RAY DIFFRACTION7chain 'C' and (resid 315 through 342 )
8X-RAY DIFFRACTION8chain 'C' and (resid 343 through 368 )
9X-RAY DIFFRACTION9chain 'C' and (resid 369 through 410 )
10X-RAY DIFFRACTION10chain 'C' and (resid 415 through 426 )

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