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- PDB-7quh: Siglec-8 in complex with therapeutic Fab AK002. -

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Basic information

Entry
Database: PDB / ID: 7quh
TitleSiglec-8 in complex with therapeutic Fab AK002.
Components
  • (Sialic acid-binding immunoglobulin-type lectin) x 2
  • Sialic 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 ...: / 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 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
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: 2.867 Å
AuthorsLenza, M.P. / Oyenarte, I. / Jimenez Barbero, J. / Ereno Orbea, J.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
Marie Sklodowska-Curie Actions, FragNET ITNEuropean Union
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 1.0May 31, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
H: Sialic acid-binding immunoglobulin-type lectin
L: Sialic acid-binding immunoglobulin-type lectin
A: Sialic acid-binding Ig-like lectin 8


Theoretical massNumber of molelcules
Total (without water)85,1253
Polymers85,1253
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4800 Å2
ΔGint-29 kcal/mol
Surface area25380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)145.343, 44.554, 111.387
Angle α, β, γ (deg.)90.000, 111.410, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Antibody Sialic acid-binding immunoglobulin-type lectin


Mass: 23603.365 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody Sialic acid-binding immunoglobulin-type lectin


Mass: 23203.768 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Protein Sialic acid-binding Ig-like lectin 8 / Siglec-8 / Sialoadhesin family member 2 / SAF-2


Mass: 38317.680 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SIGLEC8, SAF2 / Production host: Homo sapiens (human) / References: UniProt: Q9NYZ4
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 % sol: 37.63 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.2M ammonium chloride 20% PEG3350 pH6.3

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.00003 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Apr 29, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00003 Å / Relative weight: 1
ReflectionResolution: 2.867→42.32 Å / Num. obs: 14935 / % possible obs: 95.4 % / Redundancy: 6.7 % / Biso Wilson estimate: 41.5 Å2 / CC1/2: 0.985 / Rmerge(I) obs: 0.233 / Rpim(I) all: 0.097 / Net I/σ(I): 9.3
Reflection shellResolution: 2.87→2.97 Å / Rmerge(I) obs: 1.042 / Num. unique obs: 1575 / CC1/2: 0.678 / Rpim(I) all: 0.446

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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: 2.867→42.319 Å / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 27.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2836 769 5.15 %
Rwork0.2246 14166 -
obs0.2277 14935 95.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 116.89 Å2 / Biso mean: 44.8681 Å2 / Biso min: 22.92 Å2
Refinement stepCycle: final / Resolution: 2.867→42.319 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4329 0 0 0 4329
Num. residues----563
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.867-3.0880.38631640.2992949100
3.088-3.39870.32211550.27492933100
3.3987-3.89020.33751280.2301239582
3.8902-4.90.23591430.19162842100
4.9-42.3190.24071790.1963047100
Refinement TLS params.Method: refined / Origin x: -5.5232 Å / Origin y: 20.8487 Å / Origin z: 23.7127 Å
111213212223313233
T0.3189 Å20.0538 Å20.0128 Å2-0.2898 Å2-0.0554 Å2--0.2698 Å2
L1.3537 °2-0.2781 °20.5594 °2-0.1481 °2-0.2535 °2--0.2862 °2
S-0.1217 Å °-0.0592 Å °-0.0306 Å °0.0638 Å °0.0863 Å °0.0144 Å °-0.0887 Å °-0.0268 Å °0.0303 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allH1 - 220
2X-RAY DIFFRACTION1allL1 - 225
3X-RAY DIFFRACTION1allA19 - 153

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