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- PDB-7qui: Crystal structure of the N-terminal domain of Siglec-8 in complex... -

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Basic information

Entry
Database: PDB / ID: 7qui
TitleCrystal structure of the N-terminal domain of Siglec-8 in complex with sulfonamide sialoside analogue
ComponentsSialic acid-binding Ig-like lectin 8
KeywordsIMMUNE SYSTEM / Siglec / sialic acid / antibody
Function / homology
Function and homology information


sialic acid binding / transmembrane signaling receptor activity / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / carbohydrate binding / cell adhesion / signal transduction / membrane / plasma membrane
Similarity search - Function
Immunoglobulin / Immunoglobulin domain / Immunoglobulin domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. ...Immunoglobulin / Immunoglobulin domain / Immunoglobulin domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Chem-F9I / Sialic acid-binding Ig-like lectin 8
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.352 Å
AuthorsLenza, M.P. / Oyenarte, I. / Atxabal, U. / Nycholat, C. / Franconetti, A. / Quintana, J.I. / Delgado, S. / Unione, L. / Paulson, J. / Jimenez-Barbero, J. / Ereno-Orbea, J.
Funding support Spain, 3items
OrganizationGrant numberCountry
Marie Sklodowska-Curie Actions, FragNET ITN860325
European Research Council (ERC)ERC-2017-AdG, 788143-RECGLYCANMR
Other government Spain
CitationJournal: Jacs Au / Year: 2023
Title: Structures of the Inhibitory Receptor Siglec-8 in Complex with a High-Affinity Sialoside Analogue and a Therapeutic Antibody.
Authors: Lenza, M.P. / Atxabal, U. / Nycholat, C. / Oyenarte, I. / Franconetti, A. / Quintana, J.I. / Delgado, S. / Nunez-Franco, R. / Garnica Marroquin, C.T. / Coelho, H. / Unione, L. / Jimenez- ...Authors: Lenza, M.P. / Atxabal, U. / Nycholat, C. / Oyenarte, I. / Franconetti, A. / Quintana, J.I. / Delgado, S. / Nunez-Franco, R. / Garnica Marroquin, C.T. / Coelho, H. / Unione, L. / Jimenez-Oses, G. / Marcelo, F. / Schubert, M. / Paulson, J.C. / Jimenez-Barbero, J. / Ereno-Orbea, J.
History
DepositionJan 18, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 18, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 8, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Sialic acid-binding Ig-like lectin 8
A: Sialic acid-binding Ig-like lectin 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,1654
Polymers35,2772
Non-polymers1,8882
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)91.682, 91.682, 150.131
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Sialic acid-binding Ig-like lectin 8 / Siglec-8 / Sialoadhesin family member 2 / SAF-2


Mass: 17638.475 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SIGLEC8, SAF2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9NYZ4
#2: Chemical ChemComp-F9I / (2~{S},4~{S},5~{R},6~{R})-5-acetamido-2-[(2~{S},3~{R},4~{S},5~{S},6~{R})-2-[(2~{R},3~{S},4~{R},5~{R},6~{R})-5-acetamido-2-(hydroxymethyl)-4,6-bis(oxidanyl)oxan-3-yl]oxy-3,5-bis(oxidanyl)-6-(sulfooxymethyl)oxan-4-yl]oxy-6-[(1~{R},2~{R})-3-(naphthalen-2-ylsulfonylamino)-1,2-bis(oxidanyl)propyl]-4-oxidanyl-oxane-2-carboxylic acid


Mass: 943.900 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C35H49N3O23S2 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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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: 5.16 Å3/Da / Density % sol: 76.18 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.075 M Hepes pH 7.5, 15 % PEG 10000 and 25% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.71 - 2.25
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Jun 25, 2021
RadiationProtocol: LAUE / Monochromatic (M) / Laue (L): L / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.711
22.251
ReflectionResolution: 3.35→45.84 Å / Num. obs: 10954 / % possible obs: 99.9 % / Redundancy: 2 % / Biso Wilson estimate: 126.2 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.163 / Rpim(I) all: 0.037 / Net I/σ(I): 20.4
Reflection shellResolution: 3.35→3.47 Å / Rmerge(I) obs: 2.123 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 1082 / CC1/2: 0.686 / Rpim(I) all: 0.476

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PDB_EXTRACT3.27data extraction
autoPROCdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7QU6

7qu6


Resolution: 3.352→42.336 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 31.1 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2921 546 4.98 %
Rwork0.2648 10408 -
obs0.2662 10954 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 223.45 Å2 / Biso mean: 126.7064 Å2 / Biso min: 84.39 Å2
Refinement stepCycle: final / Resolution: 3.352→42.336 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2163 0 126 0 2289
Biso mean--120.38 --
Num. residues----266
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
3.352-3.68910.33481350.2972551
3.6891-4.22260.24681340.25722555
4.2226-5.31830.28621360.22432604
5.3183-42.3360.30371410.28672698
Refinement TLS params.Method: refined / Origin x: -7.9747 Å / Origin y: 34.5283 Å / Origin z: 11.8854 Å
111213212223313233
T0.6358 Å2-0.0104 Å2-0.0981 Å2-1.1246 Å2-0.1338 Å2--0.8652 Å2
L3.9233 °2-1.6663 °2-3.5509 °2-0.8681 °21.1029 °2--3.4065 °2
S-0.0824 Å °0.3168 Å °-0.1604 Å °-0.0947 Å °-0.2216 Å °0.3689 Å °0.1574 Å °-0.9261 Å °0.2474 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allB22 - 156
2X-RAY DIFFRACTION1allB201
3X-RAY DIFFRACTION1allA22 - 201

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