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- PDB-8q1x: Structural analysis of PLD3 reveals insights into the mechanism o... -

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Basic information

Entry
Database: PDB / ID: 8q1x
TitleStructural analysis of PLD3 reveals insights into the mechanism of lysosomal 5' exonuclease-mediated nucleic acid degradation
Components5'-3' exonuclease PLD3
KeywordsDNA BINDING PROTEIN / PLD3 / structural biology / lysosome / DNA/RNA degradation / phospholipase D / 5' exonuclease
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
: / PHOSPHATE ION / THYMIDINE-5'-THIOPHOSPHATE / 5'-3' exonuclease PLD3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsRoske, Y. / Daumke, O. / Damme, M.
Funding support Germany, 1items
OrganizationGrant numberCountry
Alzheimer Forschung Initiative e.V. Germany
CitationJournal: Nucleic Acids Res. / Year: 2024
Title: Structural analysis of PLD3 reveals insights into the mechanism of lysosomal 5' exonuclease-mediated nucleic acid degradation.
Authors: Roske, Y. / Cappel, C. / Cremer, N. / Hoffmann, P. / Koudelka, T. / Tholey, A. / Heinemann, U. / Daumke, O. / Damme, M.
History
DepositionAug 1, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 6, 2023Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _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)102,48736
Polymers96,3802
Non-polymers6,10634
Water18,6281034
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11460 Å2
ΔGint-18 kcal/mol
Surface area34040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.535, 115.452, 101.335
Angle α, β, γ (deg.)90.00, 106.62, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein 5'-3' exonuclease PLD3


Mass: 48190.090 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PLD3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8IV08

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Sugars , 2 types, 4 molecules

#2: Polysaccharide alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]alpha-D- ...alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1072.964 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-6DManpa1-6[DManpa1-3]DManpa1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5]/1-1-2-2-2-2/a4-b1_b4-c1_c3-d1_c6-e1_e6-f1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#3: 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.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam 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
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE

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Non-polymers , 7 types, 1064 molecules

#4: Chemical
ChemComp-PST / THYMIDINE-5'-THIOPHOSPHATE


Type: DNA linking / Mass: 338.274 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N2O7PS
#5: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#6: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#8: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#9: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1034 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 3.52 Å3/Da / Density % sol: 65.06 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 15% PEG 4000, 0.02 M NaI, 0.9 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.98141 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 18, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98141 Å / Relative weight: 1
ReflectionResolution: 1.85→48.55 Å / Num. obs: 111313 / % possible obs: 98.4 % / Redundancy: 4.05 % / CC1/2: 0.996 / Rrim(I) all: 0.014 / Net I/σ(I): 8.13
Reflection shellResolution: 1.85→1.97 Å / Num. unique obs: 17357 / CC1/2: 0.417 / Rrim(I) all: 0.1849

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XSCALEdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→35.78 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.54 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1987 2100 1.89 %
Rwork0.1738 --
obs0.1743 111276 98.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.85→35.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6558 0 341 1034 7933
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009
X-RAY DIFFRACTIONf_angle_d0.989
X-RAY DIFFRACTIONf_dihedral_angle_d13.1511116
X-RAY DIFFRACTIONf_chiral_restr0.061132
X-RAY DIFFRACTIONf_plane_restr0.0091240
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.90.49811270.41616611X-RAY DIFFRACTION90
1.9-1.940.36861410.34927302X-RAY DIFFRACTION99
1.94-20.32461400.29937292X-RAY DIFFRACTION99
2-2.050.28791410.27587356X-RAY DIFFRACTION100
2.05-2.120.27971410.24797302X-RAY DIFFRACTION100
2.12-2.20.24731420.22487369X-RAY DIFFRACTION99
2.2-2.280.26071400.20357304X-RAY DIFFRACTION99
2.28-2.390.26631390.18987214X-RAY DIFFRACTION98
2.39-2.510.2061410.17427345X-RAY DIFFRACTION99
2.51-2.670.20191410.16817335X-RAY DIFFRACTION100
2.67-2.880.2041430.15947403X-RAY DIFFRACTION100
2.88-3.170.16751410.15137343X-RAY DIFFRACTION99
3.17-3.630.16021390.14437224X-RAY DIFFRACTION97
3.63-4.570.14351420.1227365X-RAY DIFFRACTION99
4.57-35.780.15151420.14197411X-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)
13.4210.5263-3.31011.3824-0.88344.0271-0.06440.4507-0.0652-0.1497-0.00610.2066-0.2329-0.67160.06320.39930.0658-0.10270.3211-0.02810.309-17.5178-11.027722.1996
20.8811-0.00490.12971.5956-0.09961.7754-0.0171-0.01350.2119-0.0796-0.0278-0.0054-0.5520.06030.04340.42110.0049-0.03530.1863-0.01480.2213-1.9605-1.525526.0805
33.95711.77931.03261.88420.39351.1334-0.0653-0.27930.10980.2441-0.0293-0.0028-0.2444-0.0440.09250.38050.0179-0.00110.298-0.03660.2141-5.2609-11.969643.5013
41.1017-0.4274-0.51812.62440.98432.25950.0521-0.0388-0.10290.0777-0.02190.02150.0608-0.0514-0.02890.19580.0193-0.03550.14590.01850.1498-6.5155-26.75929.8071
50.9815-0.1581-0.12211.65920.13151.7506-0.00410.104-0.0417-0.3284-0.03310.1220.0113-0.09120.03120.2680.0283-0.05190.1664-0.0070.18-6.4964-23.550917.4555
67.090.89140.1782.5964-2.38567.02420.05850.6341-0.1599-0.8694-0.4357-0.34380.38730.52780.34690.57870.04830.02010.29250.0130.25530.3689-24.62053.5297
72.07940.1631.2481.40090.00063.33870.04110.1546-0.2182-0.14080.009-0.15840.41970.2127-0.03460.35780.05360.01850.1507-0.01350.254211.9037-73.818125.9484
81.1569-0.4975-0.31723.42060.92492.92090.0246-0.0836-0.35550.0167-0.02710.21880.7744-0.28940.01230.4603-0.0878-0.01040.24980.03080.2822-0.9088-78.503932.0562
91.15830.3670.13161.30520.26630.85430.0705-0.1898-0.10950.1284-0.0627-0.09070.26550.0658-0.00690.33470.0134-0.02790.23890.02870.23199.9564-66.536638.1169
102.8194-1.447-0.67894.63710.43065.513-0.0394-0.1168-0.16690.2305-0.01570.38610.1064-0.3674-0.01680.1892-0.00060.0350.10490.0120.15353.7606-50.105526.9453
113.86850.45812.05773.86142.17913.6489-0.08390.20970.2858-0.3079-0.001-0.1523-0.25310.12970.05830.30870.01840.02510.17440.05320.18036.5607-45.350618.0392
120.64680.15840.29911.4740.18152.87060.00610.137-0.0457-0.3065-0.0029-0.04610.08010.0410.0060.25920.02130.03260.1406-0.00120.18188.4358-59.115917.5598
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 72 through 104 )
2X-RAY DIFFRACTION2chain 'A' and (resid 105 through 237 )
3X-RAY DIFFRACTION3chain 'A' and (resid 238 through 278 )
4X-RAY DIFFRACTION4chain 'A' and (resid 279 through 356 )
5X-RAY DIFFRACTION5chain 'A' and (resid 357 through 469 )
6X-RAY DIFFRACTION6chain 'A' and (resid 470 through 493 )
7X-RAY DIFFRACTION7chain 'B' and (resid 72 through 138 )
8X-RAY DIFFRACTION8chain 'B' and (resid 139 through 203 )
9X-RAY DIFFRACTION9chain 'B' and (resid 204 through 306 )
10X-RAY DIFFRACTION10chain 'B' and (resid 307 through 343 )
11X-RAY DIFFRACTION11chain 'B' and (resid 344 through 392 )
12X-RAY DIFFRACTION12chain 'B' and (resid 393 through 492 )

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