+
Open data
-
Basic information
Entry | Database: PDB / ID: 7quh | ||||||
---|---|---|---|---|---|---|---|
Title | Siglec-8 in complex with therapeutic Fab AK002. | ||||||
![]() |
| ||||||
![]() | IMMUNE SYSTEM / siglec / sialic acid / antibody | ||||||
Function / homology | ![]() 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 | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Lenza, M.P. / Oyenarte, I. / Jimenez Barbero, J. / Ereno Orbea, J. | ||||||
Funding support | European Union, 1items
| ||||||
![]() | ![]() 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 |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 230.1 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 180.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 443.8 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 448.6 KB | Display | |
Data in XML | ![]() | 20.4 KB | Display | |
Data in CIF | ![]() | 27 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7qu6SC ![]() 7quiC S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data | Similarity search - Function & homology ![]() |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Antibody | Mass: 23603.365 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
---|---|
#2: Antibody | Mass: 23203.768 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
#3: Protein | Mass: 38317.680 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density % sol: 37.63 % |
---|---|
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 |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
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 |
| ||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() 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
| ||||||||||||||||||||||||||||||||||||||||
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
| ||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
| ||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Origin x: -5.5232 Å / Origin y: 20.8487 Å / Origin z: 23.7127 Å
| ||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|