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- PDB-9k2e: Crystal structure of mSMPDL3B-dimer -

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Basic information

Entry
Database: PDB / ID: 9k2e
TitleCrystal structure of mSMPDL3B-dimer
ComponentsAcid sphingomyelinase-like phosphodiesterase 3b
KeywordsHYDROLASE / Dimer / N-Glycosylation / GPI-anchor / Lipid-modulating phosphodiesterase.
Function / homology
Function and homology information


sphingomyelin catabolic process / membrane lipid catabolic process / sphingomyelin phosphodiesterase activity / negative regulation of toll-like receptor signaling pathway / Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases / hydrolase activity, acting on glycosyl bonds / phosphoric diester hydrolase activity / side of membrane / negative regulation of innate immune response / negative regulation of inflammatory response ...sphingomyelin catabolic process / membrane lipid catabolic process / sphingomyelin phosphodiesterase activity / negative regulation of toll-like receptor signaling pathway / Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases / hydrolase activity, acting on glycosyl bonds / phosphoric diester hydrolase activity / side of membrane / negative regulation of innate immune response / negative regulation of inflammatory response / inflammatory response / innate immune response / extracellular space / zinc ion binding / plasma membrane
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
PHOSPHATE ION / Acid sphingomyelinase-like phosphodiesterase 3b
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.02 Å
AuthorsZhang, C.G. / Hou, Y.F. / Liu, P.Y. / Fan, S.L.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)82241074 China
National Natural Science Foundation of China (NSFC)32070875 China
CitationJournal: To Be Published
Title: Membrane integrity changes upon viral infection activate sphingomyelinase SMPDL3B to restrict cGAS-STING signaling via cGAMP degradation
Authors: Zhang, C.G. / Hou, Y.F.
History
DepositionOct 17, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Oct 22, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)97,45911
Polymers96,3442
Non-polymers1,1159
Water12,124673
1
A: Acid sphingomyelinase-like phosphodiesterase 3b
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,6195
Polymers48,1721
Non-polymers4474
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area680 Å2
ΔGint-86 kcal/mol
Surface area15940 Å2
MethodPISA
2
B: Acid sphingomyelinase-like phosphodiesterase 3b
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,8406
Polymers48,1721
Non-polymers6685
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area980 Å2
ΔGint-82 kcal/mol
Surface area16050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.800, 87.430, 93.140
Angle α, β, γ (deg.)90.000, 98.510, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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


Mass: 48171.809 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Smpdl3b, Asml3b / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: P58242, Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases
#2: 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 / 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
#3: Chemical
ChemComp-ZN / ZINC ION


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


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 673 / Source method: isolated from a natural source / Formula: H2O
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: 2.12 Å3/Da / Density % sol: 42.07 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 25% PEG 3350, 0.1M BIS-TRIS [pH 5.5]

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.9791 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jan 24, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.02→39.49 Å / Num. obs: 103192 / % possible obs: 99.7 % / Redundancy: 6.5 % / Biso Wilson estimate: 22.35 Å2 / CC1/2: 0.996 / Net I/σ(I): 7.7
Reflection shellResolution: 2.02→2.07 Å / Num. unique obs: 3863 / CC1/2: 0.739

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PHENIX1.19.2_4158refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.02→39.49 Å / SU ML: 0.233 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.4077
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2339 3917 3.8 %
Rwork0.2223 99275 -
obs0.2228 103192 99.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.4 Å2
Refinement stepCycle: LAST / Resolution: 2.02→39.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6599 0 56 673 7328
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00366855
X-RAY DIFFRACTIONf_angle_d0.70459357
X-RAY DIFFRACTIONf_chiral_restr0.0451993
X-RAY DIFFRACTIONf_plane_restr0.00611220
X-RAY DIFFRACTIONf_dihedral_angle_d14.98372452
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.02-2.040.29971410.32683492X-RAY DIFFRACTION99.13
2.04-2.070.33161350.30013538X-RAY DIFFRACTION99.32
2.07-2.10.37711410.3033575X-RAY DIFFRACTION99.36
2.1-2.130.29831410.3043590X-RAY DIFFRACTION99.31
2.13-2.160.30061360.29323515X-RAY DIFFRACTION99.35
2.16-2.190.28571420.26663548X-RAY DIFFRACTION99.43
2.19-2.220.26541340.26363479X-RAY DIFFRACTION99.15
2.22-2.260.34161430.27013599X-RAY DIFFRACTION99.55
2.26-2.30.24791430.26223617X-RAY DIFFRACTION99.47
2.3-2.340.26131360.26063482X-RAY DIFFRACTION99.26
2.34-2.390.29381410.2593526X-RAY DIFFRACTION99.24
2.39-2.430.26811410.26053540X-RAY DIFFRACTION99.19
2.43-2.490.28321410.25513554X-RAY DIFFRACTION99.6
2.49-2.540.28771420.25533613X-RAY DIFFRACTION99.36
2.55-2.610.25391390.23943476X-RAY DIFFRACTION99.23
2.61-2.680.28391410.23653619X-RAY DIFFRACTION99.55
2.68-2.760.28261380.23763478X-RAY DIFFRACTION99.48
2.76-2.850.24421440.23623575X-RAY DIFFRACTION99.33
2.85-2.950.26251370.22773536X-RAY DIFFRACTION99.7
2.95-3.070.22761390.22873543X-RAY DIFFRACTION99.35
3.07-3.210.22761430.2143583X-RAY DIFFRACTION98.99
3.21-3.380.24891370.20123564X-RAY DIFFRACTION99.38
3.38-3.590.20391380.19273519X-RAY DIFFRACTION99.29
3.59-3.860.16781400.17353553X-RAY DIFFRACTION99.35
3.86-4.250.16891450.16893553X-RAY DIFFRACTION99.44
4.25-4.870.17961400.16583522X-RAY DIFFRACTION99.32
4.87-6.130.18231350.18643557X-RAY DIFFRACTION99.38
6.13-39.490.19711440.20013529X-RAY DIFFRACTION98.74

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