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- PDB-8v5t: Crystal structure of Alzheimers disease phospholipase D3 -

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Basic information

Entry
Database: PDB / ID: 8v5t
TitleCrystal structure of Alzheimers disease phospholipase D3
Components5'-3' exonuclease PLD3
KeywordsDNA BINDING PROTEIN / Exonuclease / Alzheimer's Disease
Function / homology
Function and homology information


spleen exonuclease / Synthesis of PG / single-stranded DNA 5'-3' DNA exonuclease activity / myotube differentiation / Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases / phospholipase D activity / regulation of cytokine production involved in inflammatory response / immune system process / Role of phospholipids in phagocytosis / lysosomal lumen ...spleen exonuclease / Synthesis of PG / single-stranded DNA 5'-3' DNA exonuclease activity / myotube differentiation / Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases / phospholipase D activity / regulation of cytokine production involved in inflammatory response / immune system process / Role of phospholipids in phagocytosis / lysosomal lumen / lipid metabolic process / late endosome membrane / early endosome membrane / inflammatory response / Golgi membrane / lysosomal membrane / endoplasmic reticulum membrane / extracellular exosome
Similarity search - Function
PLD-like domain / PLD-like domain / : / Phospholipase D. Active site motifs. / Phospholipase D/Transphosphatidylase / Phospholipase D phosphodiesterase active site profile.
Similarity search - Domain/homology
5'-3' exonuclease PLD3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsIshii, K. / Hermans, S.J. / Nero, T.L. / Gorman, M.A. / Parker, M.W.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Febs J. / Year: 2024
Title: Crystal structure of Alzheimer's disease phospholipase D3 provides a molecular basis for understanding its normal and pathological functions.
Authors: Ishii, K. / Hermans, S.J. / Georgopoulou, M.E. / Nero, T.L. / Hancock, N.C. / Crespi, G.A.N. / Gorman, M.A. / Gooi, J.H. / Parker, M.W.
History
DepositionDec 1, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 9, 2024Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 5'-3' exonuclease PLD3
B: 5'-3' exonuclease PLD3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,45319
Polymers109,5182
Non-polymers2,93517
Water6,972387
1
A: 5'-3' exonuclease PLD3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,46112
Polymers54,7591
Non-polymers1,70111
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: 5'-3' exonuclease PLD3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,9927
Polymers54,7591
Non-polymers1,2336
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)205.137, 60.566, 111.501
Angle α, β, γ (deg.)90.000, 98.720, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: Protein 5'-3' exonuclease PLD3


Mass: 54759.074 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PLD3 / Cell line (production host): Expi293 / Production host: Homo sapiens (human) / References: UniProt: Q8IV08
#2: Polysaccharide
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 387 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 3.13 Å3/Da / Density % sol: 60.65 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.17 M ammonium sulfate 15% (v/v) glycerol 25% (w/v) PEG 4000
Temp details: Room Temperature

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 16, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.3→48.96 Å / Num. obs: 112535 / % possible obs: 99.03 % / Redundancy: 3.4 % / Biso Wilson estimate: 50.55 Å2 / CC1/2: 0.997 / Rpim(I) all: 0.042 / Net I/σ(I): 10.2
Reflection shellResolution: 2.3→2.36 Å / Redundancy: 3.3 % / Mean I/σ(I) obs: 1.6 / Num. unique obs: 712 / CC1/2: 0.683 / Rpim(I) all: 0.458 / % possible all: 96.9

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→48.96 Å / SU ML: 0.3207 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 25.3371
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2094 5526 4.91 %
Rwork0.1853 107009 -
obs0.1865 112535 95.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 58.63 Å2
Refinement stepCycle: LAST / Resolution: 2.3→48.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6530 0 180 387 7097
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00956871
X-RAY DIFFRACTIONf_angle_d1.14679379
X-RAY DIFFRACTIONf_chiral_restr0.05491048
X-RAY DIFFRACTIONf_plane_restr0.0081202
X-RAY DIFFRACTIONf_dihedral_angle_d6.5871964
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.330.36711870.35223666X-RAY DIFFRACTION95.51
2.33-2.350.31461830.33253475X-RAY DIFFRACTION94.77
2.35-2.380.3462030.32093515X-RAY DIFFRACTION93.89
2.38-2.410.3431910.32033563X-RAY DIFFRACTION95.67
2.41-2.440.31711760.2993638X-RAY DIFFRACTION97.05
2.44-2.480.34511620.29473635X-RAY DIFFRACTION96.84
2.48-2.510.32161860.28753627X-RAY DIFFRACTION96.97
2.51-2.550.29571910.28063628X-RAY DIFFRACTION97.13
2.55-2.590.29591920.27313626X-RAY DIFFRACTION97.3
2.59-2.630.3091890.25813688X-RAY DIFFRACTION97.73
2.63-2.680.26212110.24423518X-RAY DIFFRACTION97.13
2.68-2.730.27641550.24623696X-RAY DIFFRACTION97.03
2.73-2.780.31421580.243671X-RAY DIFFRACTION97.33
2.78-2.840.25571680.24093668X-RAY DIFFRACTION97.46
2.84-2.90.27581910.23923645X-RAY DIFFRACTION97.14
2.9-2.970.27371970.22943613X-RAY DIFFRACTION97.17
2.97-3.040.22022010.22213636X-RAY DIFFRACTION96.89
3.04-3.120.25382100.20763482X-RAY DIFFRACTION95.95
3.12-3.210.19962070.19813559X-RAY DIFFRACTION95.92
3.21-3.320.23211560.19523597X-RAY DIFFRACTION95.16
3.32-3.440.20121620.19533477X-RAY DIFFRACTION92.78
3.44-3.570.23271920.18873558X-RAY DIFFRACTION94.27
3.57-3.740.21081970.16053443X-RAY DIFFRACTION92.93
3.74-3.930.18231900.16083421X-RAY DIFFRACTION92.92
3.93-4.180.1581510.13583542X-RAY DIFFRACTION93.73
4.18-4.50.15551900.13113432X-RAY DIFFRACTION92.56
4.5-4.950.12871760.12093453X-RAY DIFFRACTION91.99
4.95-5.670.17432040.14443477X-RAY DIFFRACTION93.17
5.67-7.140.19281800.15963493X-RAY DIFFRACTION93.87
7.14-48.960.16521700.15863567X-RAY DIFFRACTION94.97

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