+
Open data
-
Basic information
Entry | Database: PDB / ID: 7zoz | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of Siglec-15 in complex with Fab | |||||||||
![]() |
| |||||||||
![]() | IMMUNE SYSTEM / sialic acid / siglec / cancer | |||||||||
Function / homology | ![]() regulation of osteoclast development / regulation of bone resorption / DAP12 interactions / regulation of actin cytoskeleton organization / protein-containing complex / plasma membrane Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Lenza, M.P. / Oyenarte, I. / Jimenez-Barbero, J. / Ereno-Orbea, J. | |||||||||
Funding support | European Union, ![]()
| |||||||||
![]() | ![]() Title: Structural insights into Siglec-15 reveal glycosylation dependency for its interaction with T cells through integrin CD11b. Authors: Lenza, M.P. / Egia-Mendikute, L. / Antonana-Vildosola, A. / Soares, C.O. / Coelho, H. / Corzana, F. / Bosch, A. / Manisha, P. / Quintana, J.I. / Oyenarte, I. / Unione, L. / Moure, M.J. / ...Authors: Lenza, M.P. / Egia-Mendikute, L. / Antonana-Vildosola, A. / Soares, C.O. / Coelho, H. / Corzana, F. / Bosch, A. / Manisha, P. / Quintana, J.I. / Oyenarte, I. / Unione, L. / Moure, M.J. / Azkargorta, M. / Atxabal, U. / Sobczak, K. / Elortza, F. / Sutherland, J.D. / Barrio, R. / Marcelo, F. / Jimenez-Barbero, J. / Palazon, A. / Ereno-Orbea, J. | |||||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 248.7 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 194.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 435.5 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 436.6 KB | Display | |
Data in XML | ![]() | 23.9 KB | Display | |
Data in CIF | ![]() | 34.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7zorC ![]() 5vkkS C: citing same article ( S: Starting model for refinement |
---|---|
Similar structure data | Similarity search - Function & homology ![]() |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 33598.988 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
---|---|
#2: Antibody | Mass: 24378.148 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
#3: Antibody | Mass: 23765.467 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.05 Å3/Da / Density % sol: 39.96 % |
---|---|
Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / Details: 20 % PEG 3350 0.2 M Calcium Chloride |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Sep 11, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97925 Å / Relative weight: 1 |
Reflection | Resolution: 2.104→106.342 Å / Num. obs: 37172 / % possible obs: 99.8 % / Redundancy: 6.5 % / Biso Wilson estimate: 33.79 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.078 / Rpim(I) all: 0.033 / Rrim(I) all: 0.084 / Net I/σ(I): 15.1 |
Reflection shell | Resolution: 2.104→2.18 Å / Rmerge(I) obs: 0.633 / Num. unique obs: 1824 / CC1/2: 0.835 / Rpim(I) all: 0.307 / Rrim(I) all: 0.707 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 5vkk Resolution: 2.104→106.341 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 23.34 / 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: 127.58 Å2 / Biso mean: 40.4562 Å2 / Biso min: 17 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.104→106.341 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Origin x: -37.9702 Å / Origin y: 1.4837 Å / Origin z: 14.5035 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|