+Open data
-Basic information
Entry | Database: PDB / ID: 7qu6 | |||||||||
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Title | Crystal structure of the N-terminal domain of Siglec-8 | |||||||||
Components | Sialic acid-binding Ig-like lectin 8 | |||||||||
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: 2.34 Å | |||||||||
Authors | Lenza, 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 support | European Union, Spain, 2items
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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 | 7qu6.cif.gz | 352.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7qu6.ent.gz | 287.1 KB | Display | PDB format |
PDBx/mmJSON format | 7qu6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7qu6_validation.pdf.gz | 470.9 KB | Display | wwPDB validaton report |
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Full document | 7qu6_full_validation.pdf.gz | 477 KB | Display | |
Data in XML | 7qu6_validation.xml.gz | 33 KB | Display | |
Data in CIF | 7qu6_validation.cif.gz | 45.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qu/7qu6 ftp://data.pdbj.org/pub/pdb/validation_reports/qu/7qu6 | HTTPS FTP |
-Related structure data
Related structure data | 7quhC 7quiC 2n7aS 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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Unit cell |
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-Components
#1: Protein | 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 / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.02 Å3/Da / Density % sol: 39.01 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 0.1 M Bis-Tris HCl pH 6.5, and 27% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97918 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 28, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 |
Reflection | Resolution: 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 shell | Resolution: 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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 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
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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: 93.34 Å2 / Biso mean: 39.4992 Å2 / Biso min: 16.37 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.34→83.758 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: -17.4814 Å / Origin y: 6.4114 Å / Origin z: -41.8436 Å
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Refinement TLS group |
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