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- PDB-8w6p: Crystal structure of dimeric murine SMPDL3A -

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Basic information

Entry
Database: PDB / ID: 8w6p
TitleCrystal structure of dimeric murine SMPDL3A
ComponentsAcid sphingomyelinase-like phosphodiesterase 3a
KeywordsHYDROLASE / innate immunity / lipid metabolism
Function / homology
Function and homology information


nucleoside triphosphate catabolic process / Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases / phosphoric diester hydrolase activity / negative regulation of cGAS/STING signaling pathway / nucleoside-triphosphate phosphatase / ATP hydrolysis activity / extracellular space / extracellular region / zinc ion binding
Similarity search - Function
Acid sphingomyelinase-like phosphodiesterase, predicted / Acid sphingomyelinase/endopolyphosphatase, metallophosphatase domain / Sphingomyelin phosphodiesterase, C-terminal domain / Acid sphingomyelin phosphodiesterase C-terminal region / Calcineurin-like phosphoesterase domain, ApaH type / Calcineurin-like phosphoesterase / Metallo-dependent phosphatase-like
Similarity search - Domain/homology
alpha-L-fucopyranose / PHOSPHATE ION / Chem-YA4 / Cyclic GMP-AMP phosphodiesterase SMPDL3A
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.91 Å
AuthorsZhang, C. / Liu, P. / Fan, S. / Hou, Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32070875 China
CitationJournal: Immunity / Year: 2023
Title: SMPDL3A is a cGAMP-degrading enzyme induced by LXR-mediated lipid metabolism to restrict cGAS-STING DNA sensing.
Authors: Hou, Y. / Wang, Z. / Liu, P. / Wei, X. / Zhang, Z. / Fan, S. / Zhang, L. / Han, F. / Song, Y. / Chu, L. / Zhang, C.
History
DepositionAug 29, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Dec 20, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Acid sphingomyelinase-like phosphodiesterase 3a
B: Acid sphingomyelinase-like phosphodiesterase 3a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,21019
Polymers93,3292
Non-polymers3,88117
Water14,484804
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)122.225, 122.225, 79.557
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Acid sphingomyelinase-like phosphodiesterase 3a / ASM-like phosphodiesterase 3a


Mass: 46664.617 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Smpdl3a, Asml3a / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: P70158, Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases

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Sugars , 5 types, 11 molecules

#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.: 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
#3: Polysaccharide alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 367.349 Da / Num. of mol.: 1 / Source method: obtained synthetically
DescriptorTypeProgram
LFucpa1-6DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-2/a6-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(6+1)][a-L-Fucp]{}}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.: 1 / Source method: obtained synthetically
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
#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.: 6 / Source method: obtained synthetically / Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
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
#8: Sugar ChemComp-FUC / alpha-L-fucopyranose / alpha-L-fucose / 6-deoxy-alpha-L-galactopyranose / L-fucose / fucose


Type: L-saccharide, alpha linking / Mass: 164.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H12O5 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
LFucpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-L-fucopyranoseCOMMON NAMEGMML 1.0
a-L-FucpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
FucSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 4 types, 810 molecules

#5: Chemical ChemComp-YA4 / [(2~{R},3~{S},4~{S})-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-sulfanyl-phosphinic acid


Type: RNA linking / Mass: 230.176 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H11O6PS / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#9: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 804 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 3.08 Å3/Da / Density % sol: 60.1 %
Crystal growTemperature: 291 K / Method: vapor diffusion
Details: 0.1 M sodium citrate [pH 5.5], 0.2M ammonium sulfate and 30% PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: Mar 16, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.91→20.27 Å / Num. obs: 89995 / % possible obs: 98.6 % / Redundancy: 7.5 % / Biso Wilson estimate: 27 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.101 / Net I/σ(I): 17.9
Reflection shellResolution: 1.91→1.94 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.768 / Mean I/σ(I) obs: 1 / Num. unique obs: 3909 / CC1/2: 0.597 / % possible all: 85.1

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Processing

Software
NameVersionClassification
PHENIX(1.18.2_3874: ???)refinement
PDB_EXTRACTdata extraction
PHENIXmodel building
PHENIXphasing
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.91→20.27 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.05 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2462 2001 2.23 %
Rwork0.2176 --
obs0.2182 89592 98.02 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.91→20.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6612 0 202 805 7619
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.017011
X-RAY DIFFRACTIONf_angle_d1.2619577
X-RAY DIFFRACTIONf_dihedral_angle_d7.8441010
X-RAY DIFFRACTIONf_chiral_restr0.0611109
X-RAY DIFFRACTIONf_plane_restr0.0081195
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.91-1.950.40691170.33815136X-RAY DIFFRACTION81
1.95-2.010.33111390.28855977X-RAY DIFFRACTION93
2.01-2.070.35071470.26996306X-RAY DIFFRACTION100
2.07-2.130.30231420.25566331X-RAY DIFFRACTION100
2.13-2.210.27431440.2546375X-RAY DIFFRACTION100
2.21-2.30.26251460.24216344X-RAY DIFFRACTION100
2.3-2.40.31571460.24466361X-RAY DIFFRACTION100
2.4-2.530.30021440.24126335X-RAY DIFFRACTION100
2.53-2.690.25911440.24366361X-RAY DIFFRACTION100
2.69-2.890.2231460.23026363X-RAY DIFFRACTION100
2.89-3.180.24071500.22456404X-RAY DIFFRACTION100
3.18-3.640.24191400.19156384X-RAY DIFFRACTION100
3.64-4.580.19431480.18196408X-RAY DIFFRACTION100
4.58-20.270.20381480.18176506X-RAY DIFFRACTION99

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