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- PDB-8v06: Crystal structure of mouse PLD3 co-crystallized with 5'Pi-ssDNA f... -

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Basic information

Entry
Database: PDB / ID: 8v06
TitleCrystal structure of mouse PLD3 co-crystallized with 5'Pi-ssDNA for 9 days
Components(5'-3' exonuclease ...) x 2
KeywordsHYDROLASE / PLD3 / phospholipase / phosphohistidine / nuclease
Function / homology
Function and homology information


spleen exonuclease / single-stranded DNA 5'-3' DNA exonuclease activity / myotube differentiation / Role of phospholipids in phagocytosis / phospholipase D activity / regulation of cytokine production involved in inflammatory response / lysosomal lumen / late endosome membrane / early endosome membrane / inflammatory response ...spleen exonuclease / single-stranded DNA 5'-3' DNA exonuclease activity / myotube differentiation / Role of phospholipids in phagocytosis / phospholipase D activity / regulation of cytokine production involved in inflammatory response / lysosomal lumen / late endosome membrane / early endosome membrane / inflammatory response / lysosomal membrane / Golgi membrane / innate immune response / endoplasmic reticulum membrane
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 / 5'-3' exonuclease PLD3
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.73 Å
AuthorsYuan, M. / Wilson, I.A.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI142945 United States
National Institutes of Health/National Institute on Aging (NIH/NIA)AG070775 United States
CitationJournal: Structure / Year: 2024
Title: Structural and mechanistic insights into disease-associated endolysosomal exonucleases PLD3 and PLD4.
Authors: Yuan, M. / Peng, L. / Huang, D. / Gavin, A. / Luan, F. / Tran, J. / Feng, Z. / Zhu, X. / Matteson, J. / Wilson, I.A. / Nemazee, D.
History
DepositionNov 17, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 13, 2024Provider: repository / Type: Initial release
Revision 1.1Apr 17, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jun 19, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)211,69314
Polymers207,5834
Non-polymers4,11110
Water3,369187
1
A: 5'-3' exonuclease PLD3
B: 5'-3' exonuclease PLD3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,9268
Polymers103,7912
Non-polymers2,1356
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5500 Å2
ΔGint16 kcal/mol
Surface area32270 Å2
MethodPISA
2
C: 5'-3' exonuclease PLD3
D: 5'-3' exonuclease PLD3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,7676
Polymers103,7912
Non-polymers1,9764
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4850 Å2
ΔGint13 kcal/mol
Surface area32870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.155, 54.191, 202.774
Angle α, β, γ (deg.)96.61, 89.16, 90.10
Int Tables number1
Space group name H-MP1

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Components

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5'-3' exonuclease ... , 2 types, 4 molecules ACBD

#1: Protein 5'-3' exonuclease PLD3


Mass: 51935.160 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Pld3 / Production host: Homo sapiens (human) / References: UniProt: O35405
#2: Protein 5'-3' exonuclease PLD3


Mass: 51856.188 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Pld3 / Production host: Homo sapiens (human) / References: UniProt: O35405

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Sugars , 4 types, 8 molecules

#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
#4: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}LINUCSPDB-CARE
#5: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1235.105 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpa1-6[DManpa1-3]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,7,6/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3-3/a4-b1_b4-c1_c3-d1_c6-e1_e3-f1_e6-g1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#6: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 2 types, 189 molecules

#7: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 187 / 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: 2.85 Å3/Da / Density % sol: 56.84 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop
Details: 1.6 M ammonium sulfate, 0.5 mM magnesium chloride, 0.1 M citric acid, pH 4.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D /