+Open data
-Basic information
Entry | Database: PDB / ID: 7quh | ||||||
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Title | Siglec-8 in complex with therapeutic Fab AK002. | ||||||
Components |
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Keywords | IMMUNE 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 | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.867 Å | ||||||
Authors | Lenza, M.P. / Oyenarte, I. / Jimenez Barbero, J. / Ereno Orbea, J. | ||||||
Funding support | European Union, 1items
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Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7quh.cif.gz | 230.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7quh.ent.gz | 180.6 KB | Display | PDB format |
PDBx/mmJSON format | 7quh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7quh_validation.pdf.gz | 443.8 KB | Display | wwPDB validaton report |
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Full document | 7quh_full_validation.pdf.gz | 448.6 KB | Display | |
Data in XML | 7quh_validation.xml.gz | 20.4 KB | Display | |
Data in CIF | 7quh_validation.cif.gz | 27 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qu/7quh ftp://data.pdbj.org/pub/pdb/validation_reports/qu/7quh | HTTPS FTP |
-Related structure data
Related structure data | 7qu6SC 7quiC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Antibody | 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) |
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#2: Antibody | 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 | 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 |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density % sol: 37.63 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.2M ammonium chloride 20% PEG3350 pH6.3 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.00003 Å |
Detector | Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Apr 29, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.00003 Å / Relative weight: 1 |
Reflection | Resolution: 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 shell | Resolution: 2.87→2.97 Å / Rmerge(I) obs: 1.042 / Num. unique obs: 1575 / CC1/2: 0.678 / Rpim(I) all: 0.446 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 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
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 116.89 Å2 / Biso mean: 44.8681 Å2 / Biso min: 22.92 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.867→42.319 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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Refinement TLS params. | Method: refined / Origin x: -5.5232 Å / Origin y: 20.8487 Å / Origin z: 23.7127 Å
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Refinement TLS group |
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