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- PDB-9iui: Crystal structure of PSD-95 GK domain in complex with GK_FingR -

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Basic information

Entry
Database: PDB / ID: 9iui
TitleCrystal structure of PSD-95 GK domain in complex with GK_FingR
Components
  • Disks large homolog 4
  • FingR targeting PSD-95
KeywordsPROTEIN BINDING / Protein complex
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 / regulation of grooming behavior / structural constituent of postsynaptic density / synaptic vesicle maturation ...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 / regulation of grooming behavior / structural constituent of postsynaptic density / synaptic vesicle maturation / positive regulation of neuron projection arborization / receptor localization to synapse / vocalization behavior / neuron spine / cerebellar mossy fiber / AMPA glutamate receptor clustering / protein localization to synapse / positive regulation of dendrite morphogenesis / proximal dendrite / dendritic branch / Trafficking of AMPA receptors / LGI-ADAM interactions / Activation of Ca-permeable Kainate Receptor / dendritic spine morphogenesis / negative regulation of receptor internalization / juxtaparanode region of axon / frizzled binding / acetylcholine receptor binding / neuron projection terminus / regulation of NMDA receptor activity / dendritic spine organization / cellular response to potassium ion / RAF/MAP kinase cascade / positive regulation of synapse assembly / beta-2 adrenergic receptor binding / NMDA selective glutamate receptor signaling pathway / Synaptic adhesion-like molecules / neuromuscular process controlling balance / neurotransmitter receptor localization to postsynaptic specialization membrane / cortical cytoskeleton / locomotory exploration behavior / AMPA glutamate receptor complex / excitatory synapse / kinesin binding / social behavior / regulation of neuronal synaptic plasticity / glutamate receptor binding / positive regulation of excitatory postsynaptic potential / Unblocking of NMDA receptors, glutamate binding and activation / D1 dopamine receptor binding / positive regulation of synaptic transmission / regulation of postsynaptic membrane neurotransmitter receptor levels / ionotropic glutamate receptor binding / dendrite cytoplasm / synaptic membrane / cell periphery / PDZ domain binding / neuromuscular junction / establishment of protein localization / regulation of long-term neuronal synaptic plasticity / cell-cell adhesion / postsynaptic density membrane / cerebral cortex development / kinase binding / synaptic vesicle / cell-cell junction / 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 / dendrite / synapse / protein kinase binding / protein-containing complex 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 / 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 nucleoside triphosphate hydrolase
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Disks large homolog 4
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
unclassified sequences (unknown)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 Å
AuthorsZhu, S. / Cai, Q. / Zhang, M.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Mol.Cell / Year: 2025
Title: Modulating synaptic glutamate receptors by targeting network nodes of the postsynaptic density condensate.
Authors: Jia, B. / Zhu, S. / Shen, Z. / Chen, X. / Li, H. / Zhao, S. / Cai, Q. / Wang, Y. / Wang, Z. / Nicoll, R.A. / Lu, Y. / Zhang, M.
History
DepositionJul 21, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jul 23, 2025Provider: repository / Type: Initial release
Revision 1.1Aug 20, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Aug 27, 2025Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Sep 10, 2025Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Disks large homolog 4
B: FingR targeting PSD-95
C: Disks large homolog 4
D: FingR targeting PSD-95
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,9778
Polymers64,4934
Non-polymers4854
Water4,306239
1
A: Disks large homolog 4
B: FingR targeting PSD-95


Theoretical massNumber of molelcules
Total (without water)32,2462
Polymers32,2462
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2250 Å2
ΔGint-8 kcal/mol
Surface area13970 Å2
MethodPISA
2
C: Disks large homolog 4
D: FingR targeting PSD-95
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,7316
Polymers32,2462
Non-polymers4854
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3050 Å2
ΔGint-9 kcal/mol
Surface area13370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.429, 74.987, 136.567
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 2 types, 4 molecules ACBD

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


Mass: 21690.418 Da / Num. of mol.: 2 / Fragment: GK domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Dlg4, Dlgh4, Psd95 / Production host: Escherichia coli (E. coli) / References: UniProt: P31016
#2: Protein FingR targeting PSD-95


Mass: 10555.861 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) unclassified sequences (unknown) / Production host: Escherichia coli (E. coli)

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Non-polymers , 4 types, 243 molecules

#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 239 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationN

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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: 2.64 Å3/Da / Density % sol: 53.36 %
Crystal growTemperature: 289 K / Method: vapor diffusion / pH: 5 / Details: 0.1M Sodium Citrate pH 5.0, 20% PEG 20000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 17, 2021
RadiationMonochromator: LN2-cooled DCM with Si(111) crystals / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.93→50 Å / Num. obs: 51565 / % possible obs: 98.7 % / Observed criterion σ(I): -3 / Redundancy: 13.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.138 / Rrim(I) all: 0.144 / Net I/σ(I): 12.82
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
1.93-2.042.40277760.6962.5051
2.04-2.191.53878310.8721.5981
2.19-2.360.91872710.9510.9551
2.36-2.580.51967680.9860.541
2.58-2.890.28361160.9950.2941
2.89-3.330.12754320.9990.1321
3.33-4.080.06645880.9990.0691
4.08-5.750.043365610.0451
5.75-500.035212710.0361

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XDSdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.93→49.72 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 38.2 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2782 2566 5 %
Rwork0.2387 --
obs0.2406 51363 98.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.93→49.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4370 0 32 239 4641
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054529
X-RAY DIFFRACTIONf_angle_d0.7666124
X-RAY DIFFRACTIONf_dihedral_angle_d6.362630
X-RAY DIFFRACTIONf_chiral_restr0.058667
X-RAY DIFFRACTIONf_plane_restr0.006791
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.93-1.960.51931200.47942274X-RAY DIFFRACTION84
1.96-20.44851390.44792618X-RAY DIFFRACTION96
2-2.050.43951420.42422700X-RAY DIFFRACTION100
2.05-2.10.42041420.38662695X-RAY DIFFRACTION100
2.1-2.150.40231440.35722726X-RAY DIFFRACTION100
2.15-2.210.31331430.32542723X-RAY DIFFRACTION100
2.21-2.270.35331430.30542721X-RAY DIFFRACTION100
2.27-2.340.35311400.28662668X-RAY DIFFRACTION98
2.34-2.430.29831430.27282716X-RAY DIFFRACTION100
2.43-2.530.34191450.26632731X-RAY DIFFRACTION99
2.53-2.640.28581430.27432722X-RAY DIFFRACTION99
2.64-2.780.30111440.26522763X-RAY DIFFRACTION99
2.78-2.950.33861400.25152685X-RAY DIFFRACTION99
2.95-3.180.26231460.24262773X-RAY DIFFRACTION100
3.18-3.50.26821450.22482776X-RAY DIFFRACTION100
3.5-4.010.24261450.19832758X-RAY DIFFRACTION99
4.01-5.050.22421480.16772833X-RAY DIFFRACTION100
5.05-49.720.20451540.18232915X-RAY DIFFRACTION98
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)
11.42281.2931-0.07011.6857-0.17520.79180.0133-0.23290.237-0.0492-0.15560.3046-0.2217-0.19450.09460.3730.0756-0.02910.5236-0.0130.3927-10.57617.1546-13.7661
23.2139-0.2811-0.08672.22970.13913.6395-0.2103-0.1451-0.17750.41620.07860.29960.3222-0.49810.18470.3285-0.0320.05520.5793-0.0110.4023-22.4556-9.6355-5.63
32.10830.65-0.32242.937-0.35063.043-0.3389-0.0483-0.0005-0.17950.07020.41760.3536-0.48570.34570.4023-0.08720.02750.53920.02020.4431-15.2949-8.4296-12.622
41.90680.47780.20133.5943-0.53754.1549-0.42090.1307-0.3368-0.32190.068-0.59210.394-0.1930.29670.38710.01160.1050.42370.03660.4705-8.7487-1.5808-17.8974
52.38850.2773-0.49341.01470.30274.1681-0.067-0.17960.0670.0215-0.0015-0.1379-0.23150.32310.07820.3103-0.0278-0.00660.38770.04440.32593.71017.2414-12.2029
61.858-0.4098-0.94533.041-0.77016.1487-0.5652-0.78310.56840.1011-0.04660.0941-1.082-0.074-0.01360.842-0.2307-0.14031.2454-0.18670.6123-8.273811.429316.2639
71.1050.3889-1.28691.2046-0.67632.69690.3659-1.121-0.2970.05360.4130.1634-0.7726-0.385-0.38240.46580.01370.05421.26050.05490.4613-14.92585.372521.5816
81.57250.12210.90880.42350.9122.1130.6731-0.2330.4508-0.0787-0.06230.0663-0.9066-0.3608-0.41780.55480.0380.00740.5598-0.10780.4729-12.177711.96921.2717
92.7517-0.75182.00052.9683-0.07464.85660.2317-1.3342-0.3239-0.2514-0.1278-0.25560.43590.1507-0.05370.3467-0.05180.03310.74580.03140.3963-12.4543-0.23177.5025
103.4696-0.7224-0.88340.2857-0.08281.3577-0.1808-0.2083-1.4580.7112-0.19880.4430.6110.2241-0.01680.95090.128-0.13761.11590.40620.9108-4.1705-9.463117.4536
111.97840.37270.01511.28650.44594.00490.2841-0.4199-0.19110.0464-0.45740.1099-0.11-0.27850.06670.4162-0.02340.08630.69630.03420.4082-17.08782.670910.0116
120.6426-0.48070.3681.51660.11310.4890.1738-1.1094-0.1670.111-0.2044-0.2790.28210.4395-0.00420.346-0.0928-0.05621.16450.13250.4699-8.9678-0.330315.829
134.57181.18162.98651.01330.51512.6334-0.0396-0.0175-0.5216-0.09180.3736-0.4844-0.17570.7359-0.22720.3614-0.01490.02990.6974-0.02180.3518-8.09020.7858-2.7691
141.3188-0.80340.79213.164-0.69815.4522-0.032-0.5692-0.04341.3345-0.5193-0.631-0.0258-0.0292-0.06560.2903-0.5638-0.33091.98720.03340.348-5.19214.861120.984
151.1492-0.6547-0.79030.98540.00920.84320.16140.3264-0.20.00910.0160.10270.0607-0.47290.45520.37310.0489-0.03390.2518-0.04970.3791-6.2896-33.0614-33.6506
161.15950.58490.1240.5210.83772.0780.04330.17990.2326-0.1065-0.10120.1995-0.6104-0.656-0.0370.39370.06940.00430.2616-0.02530.4207-12.9967-28.9168-27.9955
173.3769-0.67340.11333.1206-0.07232.9158-0.4246-0.0350.14571.07360.06910.3729-0.2964-0.77390.35720.60160.02130.1220.73920.04460.587-25.0203-40.6343-17.3157
182.3451-0.69690.11333.0761-1.01711.73130.0213-0.0968-1.0277-0.17330.30050.83810.5379-0.3267-0.47790.6488-0.09710.00120.6043-0.04320.7901-20.9747-52.1098-25.4067
192.44340.76050.06713.5506-1.05812.9638-0.2562-0.3123-0.1147-0.34750.02510.20950.4251-0.95340.22120.4581-0.0898-0.00820.5332-0.08810.4896-15.924-45.7478-28.8878
201.30750.75510.13233.2259-0.53583.4918-0.3178-0.2415-0.3822-0.35620.1375-0.59120.2871-0.30170.21860.3720.04120.1050.36130.00320.5064-9.1266-38.9706-33.891
212.4936-0.608-0.99561.5012-0.24782.8459-0.2066-0.27140.02480.1360.1068-0.1186-0.09940.78380.17860.3573-0.0094-0.00040.48640.02590.35173.1448-29.7447-26.4921
222.4188-0.3767-0.38572.84420.24965.8278-0.4194-0.7227-0.13090.1409-0.11580.07260.59631.42990.66750.34290.11840.06260.57430.10820.41577.7652-37.8845-24.0126
232.17890.3568-0.07141.87021.17572.8899-0.0640.0340.27860.0722-0.1660.0447-0.55690.18470.25320.4736-0.0191-0.00560.43410.01010.34540.3396-24.3939-33.9268
241.80830.0151-0.07274.0989-1.02824.7299-0.1435-0.39990.2380.32870.3427-0.2371-0.85940.1368-0.18890.3899-0.02830.01610.9446-0.1430.4188-11.8392-29.31291.5176
252.92631.32050.73911.75890.71433.69230.0727-0.6704-0.3491-0.035-0.0858-0.2710.15590.13160.02630.26050.090.04270.50830.01890.3547-11.2891-36.9905-8.3007
262.390.1508-0.03331.66470.19351.72870.0628-0.9764-0.32910.22580.1769-0.025-0.1660.3251-0.23740.29230.0801-0.0030.60930.05760.355-11.6731-35.7547-1.5999
274.8451.02612.80791.16950.38452.80010.19650.0787-0.59560.0228-0.0577-0.19540.03570.4061-0.02980.36890.04210.01130.5704-0.00880.3902-8.3491-36.7496-18.9245
281.5821-0.1683-0.60662.4425-2.15424.2451-0.2271-1.5923-0.00620.8097-0.8368-0.83920.0586-0.02540.41070.5136-0.1801-0.14791.05410.02490.4729-4.8996-32.66644.6438
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 533 through 566 )
2X-RAY DIFFRACTION2chain 'A' and (resid 567 through 594 )
3X-RAY DIFFRACTION3chain 'A' and (resid 595 through 621 )
4X-RAY DIFFRACTION4chain 'A' and (resid 622 through 640 )
5X-RAY DIFFRACTION5chain 'A' and (resid 641 through 713 )
6X-RAY DIFFRACTION6chain 'B' and (resid 0 through 6 )
7X-RAY DIFFRACTION7chain 'B' and (resid 7 through 15 )
8X-RAY DIFFRACTION8chain 'B' and (resid 16 through 22 )
9X-RAY DIFFRACTION9chain 'B' and (resid 23 through 32 )
10X-RAY DIFFRACTION10chain 'B' and (resid 33 through 39 )
11X-RAY DIFFRACTION11chain 'B' and (resid 40 through 53 )
12X-RAY DIFFRACTION12chain 'B' and (resid 54 through 70 )
13X-RAY DIFFRACTION13chain 'B' and (resid 71 through 81 )
14X-RAY DIFFRACTION14chain 'B' and (resid 82 through 90 )
15X-RAY DIFFRACTION15chain 'C' and (resid 533 through 543 )
16X-RAY DIFFRACTION16chain 'C' and (resid 544 through 566 )
17X-RAY DIFFRACTION17chain 'C' and (resid 567 through 579 )
18X-RAY DIFFRACTION18chain 'C' and (resid 580 through 594 )
19X-RAY DIFFRACTION19chain 'C' and (resid 595 through 621 )
20X-RAY DIFFRACTION20chain 'C' and (resid 622 through 640 )
21X-RAY DIFFRACTION21chain 'C' and (resid 641 through 666 )
22X-RAY DIFFRACTION22chain 'C' and (resid 667 through 687 )
23X-RAY DIFFRACTION23chain 'C' and (resid 688 through 713 )
24X-RAY DIFFRACTION24chain 'D' and (resid 0 through 16 )
25X-RAY DIFFRACTION25chain 'D' and (resid 17 through 45 )
26X-RAY DIFFRACTION26chain 'D' and (resid 46 through 70 )
27X-RAY DIFFRACTION27chain 'D' and (resid 71 through 81 )
28X-RAY DIFFRACTION28chain 'D' and (resid 82 through 90 )

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