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- PDB-6ird: Complex structure of INADL PDZ89 and PLCb4 C-terminal CC-PBM -

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Basic information

Entry
Database: PDB / ID: 6ird
TitleComplex structure of INADL PDZ89 and PLCb4 C-terminal CC-PBM
Components
  • 1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase
  • InaD-like protein
KeywordsHYDROLASE/PROTEIN BINDING / PDZ supramodule / phospholipase C beta / HYDROLASE-PROTEIN BINDING complex
Function / homology
Function and homology information


PLC beta mediated events / Synthesis of IP3 and IP4 in the cytosol / tight junction assembly / Tight junction interactions / microtubule organizing center organization / phosphoinositide phospholipase C / SARS-CoV-2 targets PDZ proteins in cell-cell junction / G alpha (q) signalling events / establishment of apical/basal cell polarity / phosphatidylinositol phospholipase C activity ...PLC beta mediated events / Synthesis of IP3 and IP4 in the cytosol / tight junction assembly / Tight junction interactions / microtubule organizing center organization / phosphoinositide phospholipase C / SARS-CoV-2 targets PDZ proteins in cell-cell junction / G alpha (q) signalling events / establishment of apical/basal cell polarity / phosphatidylinositol phospholipase C activity / establishment or maintenance of epithelial cell apical/basal polarity / phosphatidylinositol-mediated signaling / parallel fiber to Purkinje cell synapse / mitogen-activated protein kinase binding / apical junction complex / smooth endoplasmic reticulum / negative regulation of potassium ion transport / centriolar satellite / bicellular tight junction / lipid catabolic process / regulation of microtubule cytoskeleton organization / modulation of chemical synaptic transmission / apical part of cell / cell junction / postsynapse / postsynaptic density / intracellular signal transduction / apical plasma membrane / dendrite / glutamatergic synapse / calcium ion binding / perinuclear region of cytoplasm / extracellular exosome / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Phospholipase C-beta, conserved site / Protein of unknown function (DUF1154) / L27-2 / L27_2 / PLC-beta, PH domain / Phospholipase C-beta, C-terminal domain superfamily / PH domain / Phosphatidylinositol-4, 5-bisphosphate phosphodiesterase beta / Phosphoinositide-specific phospholipase C, EF-hand-like domain / Phosphoinositide-specific phospholipase C, efhand-like ...Phospholipase C-beta, conserved site / Protein of unknown function (DUF1154) / L27-2 / L27_2 / PLC-beta, PH domain / Phospholipase C-beta, C-terminal domain superfamily / PH domain / Phosphatidylinositol-4, 5-bisphosphate phosphodiesterase beta / Phosphoinositide-specific phospholipase C, EF-hand-like domain / Phosphoinositide-specific phospholipase C, efhand-like / Phosphoinositide phospholipase C family / Phospholipase C, phosphatidylinositol-specific, Y domain / Phosphatidylinositol-specific phospholipase C, Y domain / Phosphatidylinositol-specific phospholipase Y-box domain profile. / Phospholipase C, catalytic domain (part); domain Y / domain in receptor targeting proteins Lin-2 and Lin-7 / L27 domain / L27 domain profile. / L27 domain superfamily / Phosphatidylinositol-specific phospholipase C, X domain / Phosphatidylinositol-specific phospholipase C, X domain / Phospholipase C, catalytic domain (part); domain X / PLC-like phosphodiesterase, TIM beta/alpha-barrel domain superfamily / C2 domain / Protein kinase C conserved region 2 (CalB) / C2 domain / C2 domain profile. / PDZ domain / Pdz3 Domain / C2 domain superfamily / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / EF-hand domain pair / Roll / Mainly Beta
Similarity search - Domain/homology
: / InaD-like protein / 1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.813 Å
AuthorsYe, F. / Li, J. / Huang, Y. / Liu, W. / Zhang, M.
CitationJournal: Elife / Year: 2018
Title: An unexpected INAD PDZ tandem-mediated plc beta binding in Drosophila photo receptors.
Authors: Ye, F. / Huang, Y. / Li, J. / Ma, Y. / Xie, C. / Liu, Z. / Deng, X. / Wan, J. / Xue, T. / Liu, W. / Zhang, M.
History
DepositionNov 12, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 23, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 28, 2020Group: Database references / Derived calculations / Category: citation / struct_conn
Item: _citation.title / _struct_conn.ptnr1_auth_asym_id ..._citation.title / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: 1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase
C: InaD-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,7727
Polymers53,7872
Non-polymers9855
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3210 Å2
ΔGint-41 kcal/mol
Surface area24900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.089, 69.089, 200.375
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein 1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase


Mass: 31063.723 Da / Num. of mol.: 1 / Fragment: C-terminal CC-PBM / Mutation: K926A,K930A,K933A,K934A,K937A,K944A,K945A,K948A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Plcb4 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q91UZ1, phosphoinositide phospholipase C
#2: Protein InaD-like protein / / hINADL / Pals1-associated tight junction protein / Protein associated to tight junctions


Mass: 22723.523 Da / Num. of mol.: 1 / Fragment: PDZ89
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PATJ, INADL / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8NI35
#3: Chemical
ChemComp-AU / GOLD ION


Mass: 196.967 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Au

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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: 2.61 Å3/Da / Density % sol: 52.86 %
Crystal growTemperature: 289 K / Method: liquid diffusion / pH: 6.5
Details: 0.2M MgCl2, 0.1M BIS-TRIS pH6.5, 20% w/v Polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 14, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 14070 / % possible obs: 99.7 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.117 / Rpim(I) all: 0.048 / Rrim(I) all: 0.127 / Χ2: 1.676 / Net I/σ(I): 6.9 / Num. measured all: 100701
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.8-2.856.90.9387100.9540.3811.0150.59599.6
2.85-2.97.80.826790.9780.3090.8780.556100
2.9-2.967.60.6546950.9810.250.7010.686100
2.96-3.027.60.4936730.9850.1910.530.696100
3.02-3.087.50.4816790.9890.1870.5180.689100
3.08-3.157.40.4496900.9820.1750.4830.675100
3.15-3.237.40.3527050.9890.1380.3790.80599.9
3.23-3.327.20.3236750.9930.1280.3490.79899.9
3.32-3.427.20.2567220.9930.1020.2760.96799.6
3.42-3.536.70.2136650.9860.0880.2311.10899.8
3.53-3.656.10.1696780.9920.0710.1831.29297.8
3.65-3.87.20.167000.9930.0640.1731.3699.4
3.8-3.977.70.1477110.9960.0580.1591.775100
3.97-4.187.70.1096870.9970.0430.1181.783100
4.18-4.447.60.0986990.9980.0390.1062.20199.9
4.44-4.797.40.0917140.9980.0360.0992.596100
4.79-5.277.10.097340.9970.0380.0983.072100
5.27-6.036.90.1027180.9910.0420.113.198100
6.03-7.596.10.0857420.9950.0370.0933.88899.2
7.59-506.20.0677940.9970.0290.0735.14898.8

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACT3.24data extraction
AutoSolphasing
SHELXDphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3R0H

3r0h


Resolution: 2.813→14.997 Å / SU ML: 0.41 / Cross valid method: THROUGHOUT / σ(F): 0.31 / Phase error: 30.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3022 604 4.86 %
Rwork0.244 --
obs0.2468 12434 88.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 300.44 Å2 / Biso mean: 28.8551 Å2 / Biso min: 2.09 Å2
Refinement stepCycle: final / Resolution: 2.813→14.997 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3189 0 5 0 3194
Biso mean--152.25 --
Num. residues----434
LS refinement shellResolution: 2.8128→3.0936 Å
RfactorNum. reflection% reflection
Rfree0.3287 106 -
Rwork0.3153 1757 -
obs--54 %

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