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- PDB-6ire: Complex structure of INAD PDZ45 and NORPA CC-PBM -

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Basic information

Entry
Database: PDB / ID: 6ire
TitleComplex structure of INAD PDZ45 and NORPA CC-PBM
Components
  • 1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase
  • Inactivation-no-after-potential D protein
KeywordsHYDROLASE/PROTEIN BINDING / drosophila / visual signaling / PDZ supramodule / phosphlipase C beta / HYDROLASE-PROTEIN BINDING complex
Function / homology
Function and homology information


PLC beta mediated events / Synthesis of IP3 and IP4 in the cytosol / G alpha (q) signalling events / : / myosin III binding / detection of light stimulus involved in sensory perception / inaD signaling complex / negative regulation of compound eye retinal cell programmed cell death / negative regulation of opsin-mediated signaling pathway / rhabdomere ...PLC beta mediated events / Synthesis of IP3 and IP4 in the cytosol / G alpha (q) signalling events / : / myosin III binding / detection of light stimulus involved in sensory perception / inaD signaling complex / negative regulation of compound eye retinal cell programmed cell death / negative regulation of opsin-mediated signaling pathway / rhabdomere / positive regulation of clathrin-dependent endocytosis / mucosal immune response / phosphoinositide phospholipase C / diacylglycerol biosynthetic process / detection of chemical stimulus involved in sensory perception of bitter taste / rhodopsin mediated signaling pathway / cellular response to light stimulus / phosphatidylinositol metabolic process / phospholipid biosynthetic process / entrainment of circadian clock / thermotaxis / phosphatidylinositol phospholipase C activity / phospholipase C activity / photoreceptor cell maintenance / phosphatidylinositol-mediated signaling / myosin binding / entrainment of circadian clock by photoperiod / photoreceptor activity / phototransduction / phospholipid metabolic process / lipid catabolic process / release of sequestered calcium ion into cytosol / visual perception / adult locomotory behavior / calcium-mediated signaling / sensory perception of sound / protein localization / circadian rhythm / signaling receptor complex adaptor activity / phospholipase C-activating G protein-coupled receptor signaling pathway / calmodulin binding / calcium ion binding
Similarity search - Function
Phospholipase C-beta, conserved site / Protein of unknown function (DUF1154) / 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 ...Phospholipase C-beta, conserved site / Protein of unknown function (DUF1154) / 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 / Phosphatidylinositol-specific phospholipase X-box domain profile. / 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
1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase / Inactivation-no-after-potential D protein
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.25 Å
AuthorsYe, F. / Li, J. / Deng, X. / 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 / Category: citation / Item: _citation.title
Revision 1.2Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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
A: 1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase
B: Inactivation-no-after-potential D protein


Theoretical massNumber of molelcules
Total (without water)48,3902
Polymers48,3902
Non-polymers00
Water181
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2730 Å2
ΔGint-16 kcal/mol
Surface area21430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.946, 157.213, 60.986
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein 1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase / 1-phosphatidylinositol 4 / 5-bisphosphate phosphodiesterase beta / No receptor potential A protein ...1-phosphatidylinositol 4 / 5-bisphosphate phosphodiesterase beta / No receptor potential A protein / Phosphoinositide phospholipase C / Phosphoinositide phospholipase C-beta


Mass: 27058.801 Da / Num. of mol.: 1 / Fragment: C-terminal CC-PBM / Mutation: K880A,K884A,K887A,K888A,K891A,K898A,K899A,K902A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: norpA, PLC-beta, CG3620 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P13217, phosphoinositide phospholipase C
#2: Protein Inactivation-no-after-potential D protein


Mass: 21330.846 Da / Num. of mol.: 1 / Fragment: PDZ45
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: inaD, CG3504 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q24008
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1 / 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: 2.86 Å3/Da / Density % sol: 57 %
Crystal growTemperature: 289 K / Method: liquid diffusion
Details: 0.2M MgCl2, 0.1M TRIS pH 6.5, 25% 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: BL17U / Wavelength: 0.978 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 16, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 3.25→50 Å / Num. obs: 9527 / % possible obs: 99.6 % / Redundancy: 5.9 % / Rmerge(I) obs: 0.083 / Rpim(I) all: 0.037 / Rrim(I) all: 0.091 / Χ2: 1.478 / Net I/σ(I): 8.4 / Num. measured all: 56563
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3.25-3.315.90.8544750.6220.3810.9371.458100
3.31-3.375.90.7014740.6780.3140.7691.503100
3.37-3.4360.5124850.7510.2280.5611.492100
3.43-3.55.90.4384430.830.1960.4811.574100
3.5-3.585.80.3884740.8770.1750.4271.546100
3.58-3.665.80.3244720.9190.1470.3571.5399.8
3.66-3.755.70.2984630.9180.1360.3291.78599.8
3.75-3.855.40.2454780.9630.1160.2721.59499.6
3.85-3.975.90.2254560.9770.1010.2481.53599.6
3.97-4.096.20.1884790.9830.0830.2061.461100
4.09-4.246.10.1514560.990.0660.1651.515100
4.24-4.416.10.1134880.9940.0490.1231.62199.8
4.41-4.616.10.0934630.9940.0410.1021.5299.8
4.61-4.856.10.0924840.9970.040.1011.506100
4.85-5.166.20.0784800.9970.0340.0851.448100
5.16-5.566.10.0794840.9960.0350.0871.484100
5.56-6.1160.0734860.9970.0320.081.353100
6.11-76.10.0534790.9980.0230.0581.25899.8
7-8.815.90.0345000.9990.0150.0371.23999.6
8.81-505.30.0245080.9990.0110.0261.18994.4

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACT3.24data extraction
PHASERphasing
RefinementResolution: 3.25→32.705 Å / SU ML: 0.5 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 35.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2752 474 5.14 %
Rwork0.2252 --
obs0.2278 9219 99.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 245.95 Å2 / Biso mean: 119.1529 Å2 / Biso min: 41.69 Å2
Refinement stepCycle: final / Resolution: 3.25→32.705 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2981 0 0 1 2982
Biso mean---74.93 -
Num. residues----416
LS refinement shellResolution: 3.2502→3.72 Å
RfactorNum. reflection% reflection
Rfree0.3566 168 -
Rwork0.2584 2857 -
obs--100 %
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)
13.7456-3.077-2.04374.12752.14540.9465-0.5925-1.13690.76440.89240.99040.28110.01270.5086-0.33931.3290.26110.19131.3577-0.30250.8387-18.845516.870828.8192
24.0399-2.5792-2.15394.19932.34873.7030.1978-0.3150.36120.18540.21790.0629-0.2802-0.0496-0.30560.60170.00110.12180.6722-0.01160.363-10.40653.32915.5192
35.13020.6195-0.27590.0779-0.03410.00321.13570.83422.4434-0.14980.193-0.027-0.85160.4371-1.38692.26851.3065-0.1085-0.3033-0.63371.69266.2779-54.5705-6.977
42.5672-0.3994-1.54472.0917-0.87442.38740.23370.1907-0.1664-0.8743-0.04770.729-0.4377-0.1439-0.12850.56630.0986-0.10590.7792-0.10420.4398-14.3559-0.64447.1148
51.8177-1.81652.34721.8737-1.92225.27490.95170.5166-0.3169-0.35830.44860.587-0.289-0.7994-0.95211.46580.6682-0.13811.3411-0.43172.4877-46.663413.19125.0511
62.991.21071.12733.1572-0.23715.32170.16310.3534-0.915-0.4251-0.12980.96960.0379-0.3333-0.05171.07690.3525-0.16740.802-0.17281.4471-35.688313.829913.4083
72.85181.31984.71848.20242.7588.79441.0162-0.5903-0.12281.3669-0.06431.29450.9038-0.9426-0.93751.45790.25950.63631.07520.07041.4016-39.530118.456133.4182
86.1832-2.2844-2.91613.00650.87492.0966-0.49-0.0203-0.35430.9139-0.57531.1987-0.0706-1.64570.64591.6783-0.14580.59160.865-0.08571.3046-41.17999.766829.1614
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 862 through 933 )A862 - 933
2X-RAY DIFFRACTION2chain 'A' and (resid 934 through 1013 )A934 - 1013
3X-RAY DIFFRACTION3chain 'A' and (resid 1014 through 1023 )A1014 - 1023
4X-RAY DIFFRACTION4chain 'A' and (resid 1024 through 1095 )A1024 - 1095
5X-RAY DIFFRACTION5chain 'B' and (resid 478 through 493 )B478 - 493
6X-RAY DIFFRACTION6chain 'B' and (resid 494 through 574 )B494 - 574
7X-RAY DIFFRACTION7chain 'B' and (resid 575 through 651 )B575 - 651
8X-RAY DIFFRACTION8chain 'B' and (resid 652 through 671 )B652 - 671

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