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- PDB-9o6n: Structure of Siglec-10 -

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Basic information

Entry
Database: PDB / ID: 9o6n
TitleStructure of Siglec-10
ComponentsSialic acid-binding Ig-like lectin 10
KeywordsIMMUNE SYSTEM / Siglec / Receptor
Function / homology
Function and homology information


negative regulation of inflammatory response to wounding / sialic acid binding / phosphatase binding / SH2 domain binding / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / carbohydrate binding / adaptive immune response / cell adhesion / innate immune response / extracellular region / plasma membrane
Similarity search - Function
: / Immunoglobulin domain / Immunoglobulin I-set / Immunoglobulin I-set domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. ...: / Immunoglobulin domain / Immunoglobulin I-set / Immunoglobulin I-set domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
CITRATE ANION / Sialic acid-binding Ig-like lectin 10
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.98 Å
AuthorsMedina, E. / Ming, Q. / Tran, T.H. / Luca, V.C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM133482 United States
CitationJournal: To Be Published
Title: Structure of apo-SigLec10
Authors: Medina, E. / Ming, Q. / Tran, T.H. / Luca, V.C.
History
DepositionApr 14, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 25, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Sialic acid-binding Ig-like lectin 10
B: Sialic acid-binding Ig-like lectin 10
C: Sialic acid-binding Ig-like lectin 10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,72411
Polymers74,1293
Non-polymers1,5958
Water1629
1
A: Sialic acid-binding Ig-like lectin 10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,6754
Polymers24,7101
Non-polymers9653
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Sialic acid-binding Ig-like lectin 10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,0594
Polymers24,7101
Non-polymers3493
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Sialic acid-binding Ig-like lectin 10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,9913
Polymers24,7101
Non-polymers2812
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)83.830, 83.830, 484.400
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

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Protein , 1 types, 3 molecules ABC

#1: Protein Sialic acid-binding Ig-like lectin 10 / Siglec-10 / Siglec-like protein 2


Mass: 24709.758 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SIGLEC10, SLG2, UNQ477/PRO940 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q96LC7

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Sugars , 2 types, 2 molecules

#2: 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
#4: 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.: 1 / 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

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Non-polymers , 4 types, 15 molecules

#3: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: C6H5O7 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / 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: 3.31 Å3/Da / Density % sol: 62.89 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop
Details: 0.085 M Sodium Citrate pH 5.4, 0.17 M Ammonium Acetate, 15% v/v Glycerol, and 23% w/v PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.97741 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Dec 14, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97741 Å / Relative weight: 1
ReflectionResolution: 2.98→48.44 Å / Num. obs: 21921 / % possible obs: 99.9 % / Redundancy: 18.3 % / CC1/2: 0.997 / Rmerge(I) obs: 0.271 / Rrim(I) all: 0.279 / Net I/σ(I): 10.84
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
2.98-3.061.8315600.6961.8831
3.06-3.141.36415250.8091.4021
3.14-3.231.09315190.9151.1231
3.23-3.330.85714360.9250.881
3.33-3.440.71313970.9480.7331
3.44-3.560.56713720.9620.5831
3.56-3.70.4713300.970.4841
3.7-3.850.38512820.9880.3961
3.85-4.020.32212380.9870.3311
4.02-4.210.25711800.9940.2631
4.21-4.440.19711190.9950.2021
4.44-4.710.1810760.9950.1851
4.71-5.040.16610120.9960.171
5.04-5.440.1689550.9960.1731
5.44-5.960.1699000.9960.1741
5.96-6.660.1578060.9980.1621
6.66-7.690.1237360.9980.1271
7.69-9.420.0836370.9990.0861
9.42-13.330.0595170.9990.0611
13.33-48.440.0513240.9990.0531

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Processing

Software
NameVersionClassification
PHENIX(1.21.1_5286: ???)refinement
XSCALEdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.98→46.5 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2588 1999 9.12 %
Rwork0.2122 --
obs0.2166 21908 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.98→46.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5182 0 105 9 5296
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0095461
X-RAY DIFFRACTIONf_angle_d1.2227435
X-RAY DIFFRACTIONf_dihedral_angle_d18.2052042
X-RAY DIFFRACTIONf_chiral_restr0.064799
X-RAY DIFFRACTIONf_plane_restr0.01967
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.98-3.050.36921370.33351370X-RAY DIFFRACTION100
3.05-3.140.35641380.28791375X-RAY DIFFRACTION100
3.14-3.230.34381410.27841403X-RAY DIFFRACTION100
3.23-3.330.29121380.24951360X-RAY DIFFRACTION100
3.33-3.450.28711370.24311381X-RAY DIFFRACTION100
3.45-3.590.30071390.24561391X-RAY DIFFRACTION100
3.59-3.750.30691400.22631381X-RAY DIFFRACTION100
3.75-3.950.28731420.22151411X-RAY DIFFRACTION100
3.95-4.20.21071430.21427X-RAY DIFFRACTION100
4.2-4.520.23881400.17131401X-RAY DIFFRACTION100
4.52-4.980.22221450.16751435X-RAY DIFFRACTION100
4.98-5.70.23151450.18531451X-RAY DIFFRACTION100
5.7-7.170.22751510.21521492X-RAY DIFFRACTION100
7.18-46.50.23351630.1971631X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 7.879 Å / Origin y: -25.7882 Å / Origin z: -14.4739 Å
111213212223313233
T0.3847 Å20.0049 Å2-0.0373 Å2-0.4527 Å20.0306 Å2--0.3717 Å2
L0.2656 °20.1199 °2-0.1751 °2-0.5103 °2-0.1874 °2--0.222 °2
S-0.0211 Å °-0.0433 Å °-0.0059 Å °0.1037 Å °-0.002 Å °0.018 Å °-0.0629 Å °-0.0294 Å °0.0278 Å °
Refinement TLS groupSelection details: all

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