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- PDB-4h11: Interaction partners of PSD-93 studied by X-ray crystallography a... -

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Basic information

Entry
Database: PDB / ID: 4h11
TitleInteraction partners of PSD-93 studied by X-ray crystallography and fluorescent polarization spectroscopy
ComponentsDisks large homolog 2
KeywordsNEUROPEPTIDE / All beta PDZ / Protein interaction / PROTEIN BINDING
Function / homology
Function and homology information


retrograde axonal protein transport / negative regulation of phosphatase activity / neuronal ion channel clustering / Neurexins and neuroligins / : / anterograde axonal protein transport / structural constituent of postsynaptic density / receptor localization to synapse / cellular response to potassium ion / juxtaparanode region of axon ...retrograde axonal protein transport / negative regulation of phosphatase activity / neuronal ion channel clustering / Neurexins and neuroligins / : / anterograde axonal protein transport / structural constituent of postsynaptic density / receptor localization to synapse / cellular response to potassium ion / juxtaparanode region of axon / establishment or maintenance of epithelial cell apical/basal polarity / RAF/MAP kinase cascade / neurotransmitter receptor localization to postsynaptic specialization membrane / receptor clustering / Unblocking of NMDA receptors, glutamate binding and activation / axon cytoplasm / sensory perception of pain / PDZ domain binding / postsynaptic density membrane / neuromuscular junction / cell-cell adhesion / synaptic vesicle membrane / kinase binding / cell junction / perikaryon / chemical synaptic transmission / postsynaptic membrane / basolateral plasma membrane / protein phosphatase binding / postsynaptic density / neuron projection / neuronal cell body / dendrite / glutamatergic synapse / protein-containing complex binding / membrane / nucleus / plasma membrane / cytoplasm
Similarity search - Function
Disks Large homologue 2, SH3 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. ...Disks Large homologue 2, SH3 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. / 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
ACETATE ION / Disks large homolog 2
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.67 Å
AuthorsFiorentini, M. / Kastrup, J.S. / Gajhede, M.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2013
Title: Interaction partners of PSD-93 studied by X-ray crystallography and fluorescence polarization spectroscopy.
Authors: Fiorentini, M. / Bach, A. / Stromgaard, K. / Kastrup, J.S. / Gajhede, M.
History
DepositionSep 10, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 3, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Disks large homolog 2
B: Disks large homolog 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,3584
Polymers22,2032
Non-polymers1552
Water3,117173
1
A: Disks large homolog 2


Theoretical massNumber of molelcules
Total (without water)11,1021
Polymers11,1021
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Disks large homolog 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,2573
Polymers11,1021
Non-polymers1552
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
B: Disks large homolog 2
hetero molecules

A: Disks large homolog 2


Theoretical massNumber of molelcules
Total (without water)22,3584
Polymers22,2032
Non-polymers1552
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_545-x,y-1/2,-z+1/21
Buried area1470 Å2
ΔGint-22 kcal/mol
Surface area11520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)33.200, 45.550, 104.240
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 2 / Channel-associated protein of synapse-110 / Chapsyn-110 / Postsynaptic density protein PSD-93


Mass: 11101.501 Da / Num. of mol.: 2 / Fragment: PDZ1: unp residues 93-188
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Dlg2, Dlgh2 / Plasmid: pGEX-6P-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3)pLYsS / References: UniProt: Q63622
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 173 / 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: 1.77 Å3/Da / Density % sol: 30.7 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4.2
Details: Crystallization of PSD-93 PDZ1ext was performed using the hanging-drop vapor diffusion technique by mixing 1 microliter of a 2 mg/ml protein solution (PBS buffer) and 1 l reservoir solution ...Details: Crystallization of PSD-93 PDZ1ext was performed using the hanging-drop vapor diffusion technique by mixing 1 microliter of a 2 mg/ml protein solution (PBS buffer) and 1 l reservoir solution (0.2 M lithium sulfate, 20% PEG 1000, 0.1 M citric acid/sodium hydrogen phosphate pH 4.2. The reservoir volume was 500 microliter, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Feb 16, 2009
RadiationMonochromator: FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.67→28 Å / Num. all: 19048 / Num. obs: 19048 / % possible obs: 100 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3
Reflection shellResolution: 1.67→1.73 Å / % possible all: 99.8

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine: 1.8_1069)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.67→28 Å / SU ML: 0.15 / σ(F): 0 / Phase error: 21.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.213 974 5.16 %Random
Rwork0.1716 ---
obs0.1738 18859 99.03 %-
all-18859 --
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.67→28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1544 0 9 173 1726
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0111604
X-RAY DIFFRACTIONf_angle_d1.2532174
X-RAY DIFFRACTIONf_dihedral_angle_d13.13612
X-RAY DIFFRACTIONf_chiral_restr0.079247
X-RAY DIFFRACTIONf_plane_restr0.006293
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.67-1.7580.2771410.20822518X-RAY DIFFRACTION100
1.758-1.86820.22881440.19622502X-RAY DIFFRACTION100
1.8682-2.01240.23451480.18352527X-RAY DIFFRACTION100
2.0124-2.21480.22351160.15862573X-RAY DIFFRACTION100
2.2148-2.53510.20821380.16982592X-RAY DIFFRACTION100
2.5351-3.19330.21261600.16352568X-RAY DIFFRACTION100
3.1933-28.00550.18861270.16762605X-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)
10.48280.15620.40810.26570.05450.35540.0263-0.0490.1889-0.0245-0.07590.0943-0.2389-0.263-0.10540.20560.07760.02430.08980.05040.1431-1.713818.694634.8609
20.2484-0.07510.19240.0509-0.0330.1346-0.1144-0.0132-0.2337-0.0605-0.0221-0.04270.11010.0638-0.03020.1236-0.00730.04550.0986-0.00320.13034.73975.039237.1947
30.03770.0376-0.04370.07310.05910.17230.07510.16390.0064-0.0584-0.01860.0712-0.0804-0.34240.00370.1175-0.01570.03240.1748-0.02310.1573-8.61558.12438.8832
40.04690.01990.02320.0576-0.00990.0124-0.03230.06940.1248-0.0889-0.0394-0.1163-0.23880.0818-0.04180.127-0.0162-0.00090.0726-0.00680.10077.739514.581341.9795
50.0020.0013-0.00320.00360.00560.00740.069-0.2173-0.0226-0.00750.0137-0.04770.07460.01530.00280.11090.04630.00010.13730.02750.12479.07555.469845.138
60.35360.1680.12090.0920.09110.1293-0.0847-0.22990.189-0.1825-0.06950.01610.0756-0.0811-0.06220.13850.00190.01760.12540.00020.07720.231913.868843.8513
70.18720.11330.07410.06830.04460.02690.2251-0.1909-0.27540.0510.0786-0.26620.0340.07340.12160.2748-0.07270.02150.30830.13390.3146-4.269220.435117.8923
81.27830.22090.65460.07340.06720.401-0.0427-0.15570.2105-0.4472-0.1432-0.1493-0.0911-0.0762-0.09810.28030.03330.07010.1060.03070.1822-18.1048-4.782335.3927
90.07190.0290.05180.00330.02990.20350.0141-0.39880.06330.0789-0.04250.03780.0837-0.02710.00430.17360.02810.03690.1484-0.00010.1743-16.9352-19.243545.7718
100.6137-0.01850.2069-0.0007-0.00490.0782-0.23220.20760.1795-0.13090.2039-0.13750.23810.1734-0.03050.2040.00360.04170.15420.00090.1052-2.2461-15.895331.1911
110.1449-0.15770.06620.1217-0.0980.2227-0.0939-0.12250.0462-0.1490.07130.0179-0.0255-0.2450.03950.0680.0120.00960.0709-0.00950.0837-19.2395-14.858137.8534
120.04490.0378-0.01290.03850.01680.0215-0.0498-0.35140.1443-0.0346-0.0033-0.02880.04310.1776-00.12460.0309-0.00260.1567-0.0250.1772-5.8769-12.545544.0306
130.02320.09140.0240.38630.10710.03080.125-0.32710.2853-0.16530.00330.08280.0046-0.08370.00470.13180.00120.03220.2298-0.0040.1491-15.8041-9.245344.4513
140.006-0.01170.00180.0143-0.0070.014-0.1228-0.0563-0.06440.0418-0.0114-0.10320.07310.0102-0.00020.3234-0.11060.00810.24430.00710.1892-21.1233-2.899918.1454
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 91 through 102 )
2X-RAY DIFFRACTION2chain 'A' and (resid 103 through 132 )
3X-RAY DIFFRACTION3chain 'A' and (resid 133 through 148 )
4X-RAY DIFFRACTION4chain 'A' and (resid 149 through 162 )
5X-RAY DIFFRACTION5chain 'A' and (resid 163 through 171 )
6X-RAY DIFFRACTION6chain 'A' and (resid 172 through 184 )
7X-RAY DIFFRACTION7chain 'A' and (resid 185 through 192 )
8X-RAY DIFFRACTION8chain 'B' and (resid 92 through 102 )
9X-RAY DIFFRACTION9chain 'B' and (resid 103 through 114 )
10X-RAY DIFFRACTION10chain 'B' and (resid 115 through 126 )
11X-RAY DIFFRACTION11chain 'B' and (resid 127 through 153 )
12X-RAY DIFFRACTION12chain 'B' and (resid 154 through 171 )
13X-RAY DIFFRACTION13chain 'B' and (resid 172 through 184 )
14X-RAY DIFFRACTION14chain 'B' and (resid 185 through 192 )

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