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- PDB-7qu6: Crystal structure of the N-terminal domain of Siglec-8 -

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Basic information

Entry
Database: PDB / ID: 7qu6
TitleCrystal structure of the N-terminal domain of Siglec-8
ComponentsSialic acid-binding Ig-like lectin 8
KeywordsIMMUNE SYSTEM / Siglec / sialic acid / antibody
Function / homology
Function and homology information


sialic acid binding / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / transmembrane signaling receptor activity / 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
Sialic acid-binding Ig-like lectin 8
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.34 Å
AuthorsLenza, M.P. / Atxabal, U. / Nycholat, C.M. / Oyenarte, I. / Paulson, J.C. / Franconetti, A. / Quintana, J.I. / Unione, L. / Delgado, S. / Jimenez-Barbero, J. / Ereno-Orbea, J.
Funding supportEuropean Union, Spain, 2items
OrganizationGrant numberCountry
Marie Sklodowska-Curie Actions, FragNET ITNEuropean Union
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 17, 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

Downloads & links

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Assembly

Deposited unit
B: Sialic acid-binding Ig-like lectin 8
A: Sialic acid-binding Ig-like lectin 8
C: Sialic acid-binding Ig-like lectin 8
D: Sialic acid-binding Ig-like lectin 8
E: Sialic acid-binding Ig-like lectin 8
F: Sialic acid-binding Ig-like lectin 8


Theoretical massNumber of molelcules
Total (without water)105,8316
Polymers105,8316
Non-polymers00
Water5,495305
1
B: Sialic acid-binding Ig-like lectin 8


Theoretical massNumber of molelcules
Total (without water)17,6381
Polymers17,6381
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Sialic acid-binding Ig-like lectin 8


Theoretical massNumber of molelcules
Total (without water)17,6381
Polymers17,6381
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Sialic acid-binding Ig-like lectin 8


Theoretical massNumber of molelcules
Total (without water)17,6381
Polymers17,6381
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Sialic acid-binding Ig-like lectin 8


Theoretical massNumber of molelcules
Total (without water)17,6381
Polymers17,6381
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Sialic acid-binding Ig-like lectin 8


Theoretical massNumber of molelcules
Total (without water)17,6381
Polymers17,6381
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Sialic acid-binding Ig-like lectin 8


Theoretical massNumber of molelcules
Total (without water)17,6381
Polymers17,6381
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.075, 36.365, 167.516
Angle α, β, γ (deg.)90.000, 90.050, 90.000
Int Tables number4
Space group name H-MP1211

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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.: 6
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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 305 / Source method: isolated from a natural source / Formula: H2O

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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: 2.02 Å3/Da / Density % sol: 39.01 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 0.1 M Bis-Tris HCl pH 6.5, and 27% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 28, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.34→83.82 Å / Num. obs: 36480 / % possible obs: 99.8 % / Redundancy: 6.7 % / Biso Wilson estimate: 34.8 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.179 / Rpim(I) all: 0.075 / Net I/σ(I): 10.8
Reflection shellResolution: 2.34→2.42 Å / Redundancy: 6.1 % / Rmerge(I) obs: 1.249 / Mean I/σ(I) obs: 2.6 / Num. unique obs: 3624 / CC1/2: 0.63 / Rpim(I) all: 0.526 / % possible all: 99.6

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
XDSdata reduction
PDB_EXTRACT3.27data extraction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2N7A

2n7a


Resolution: 2.34→83.758 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 26.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2565 1913 5.24 %
Rwork0.2061 34561 -
obs0.2087 36474 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 93.34 Å2 / Biso mean: 39.4992 Å2 / Biso min: 16.37 Å2
Refinement stepCycle: final / Resolution: 2.34→83.758 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6727 0 0 305 7032
Biso mean---42.48 -
Num. residues----827
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.3403-2.39880.29521220.27582465100
2.3988-2.46370.36591710.2772388100
2.4637-2.53620.30081540.26322387100
2.5362-2.61810.30831170.25952471100
2.6181-2.71170.32541350.262427100
2.7117-2.82020.35221280.2492494100
2.8202-2.94860.3041530.23792395100
2.9486-3.10410.27961350.22072432100
3.1041-3.29850.2551320.20982527100
3.2985-3.55320.22491290.19042434100
3.5532-3.91080.21891240.18722513100
3.9108-4.47670.24561120.16152509100
4.4767-5.640.22561430.17192506100
5.64-83.7580.19911580.1989261399
Refinement TLS params.Method: refined / Origin x: -17.4814 Å / Origin y: 6.4114 Å / Origin z: -41.8436 Å
111213212223313233
T0.1861 Å2-0.0137 Å20.0412 Å2-0.1571 Å2-0.014 Å2--0.2108 Å2
L0.4555 °2-0.0711 °20.2306 °2-0.0792 °2-0.0192 °2--0.2456 °2
S0.02 Å °-0.0005 Å °-0.0412 Å °-0.0156 Å °-0.0108 Å °0.0009 Å °-0.0149 Å °0.0306 Å °-0.0026 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allB21 - 152
2X-RAY DIFFRACTION1allA21 - 152
3X-RAY DIFFRACTION1allC20 - 166
4X-RAY DIFFRACTION1allD20 - 154
5X-RAY DIFFRACTION1allE20 - 154
6X-RAY DIFFRACTION1allF21 - 166
7X-RAY DIFFRACTION1allH3 - 427

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