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- PDB-7joo: Crystal structure of ICOS in complex with antibody STIM003 and an... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7joo | |||||||||
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Title | Crystal structure of ICOS in complex with antibody STIM003 and anti-kappa VHH domain | |||||||||
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![]() | IMMUNE SYSTEM / Immune checkpoint / glycoprotein / receptor / T-cell / antibody | |||||||||
Function / homology | ![]() T cell tolerance induction / Costimulation by the CD28 family / T cell costimulation / cell-cell adhesion / Constitutive Signaling by Aberrant PI3K in Cancer / PIP3 activates AKT signaling / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / immune response / extracellular region / plasma membrane Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Rujas, E. / Sicard, T. / Julien, J.P. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural characterization of the ICOS/ICOS-L immune complex reveals high molecular mimicry by therapeutic antibodies. Authors: Rujas, E. / Cui, H. / Sicard, T. / Semesi, A. / Julien, J.P. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 172 KB | Display | ![]() |
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PDB format | ![]() | 105.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 489.6 KB | Display | ![]() |
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Full document | ![]() | 497.1 KB | Display | |
Data in XML | ![]() | 25.2 KB | Display | |
Data in CIF | ![]() | 35.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6x4gC ![]() 6x4tC ![]() 1i8lS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components
-Antibody , 3 types, 3 molecules KHL
#1: Antibody | Mass: 11326.253 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Production host: ![]() |
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#2: Antibody | Mass: 24164.895 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
#3: Antibody | Mass: 23619.229 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
-Protein / Sugars , 2 types, 2 molecules C![](data/chem/img/NAG.gif)
![](data/chem/img/NAG.gif)
#4: Protein | Mass: 14430.349 Da / Num. of mol.: 1 / Mutation: N23Q, C136A, C137A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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#6: Sugar | ChemComp-NAG / |
-Non-polymers , 2 types, 167 molecules ![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/HOH.gif)
#5: Chemical | ChemComp-GOL / |
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#7: Water | ChemComp-HOH / |
-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.67 Å3/Da / Density % sol: 54.01 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop Details: 0.2 M di-sodium hydrogen phosphate and 20% (w/v) polyethylene glycol 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 6, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979341 Å / Relative weight: 1 |
Reflection | Resolution: 2.38→40 Å / Num. obs: 30150 / % possible obs: 99.2 % / Redundancy: 6.6 % / CC1/2: 0.997 / Rmerge(I) obs: 0.109 / Rpim(I) all: 0.045 / Net I/σ(I): 13.3 |
Reflection shell | Resolution: 2.38→2.48 Å / Redundancy: 6 % / Rmerge(I) obs: 0.608 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 3223 / CC1/2: 0.732 / Rpim(I) all: 0.258 / % possible all: 94 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1I8L, internal database Resolution: 2.4→28.48 Å / SU ML: 0.4469 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 32.9037 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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 mean: 51.5 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→28.48 Å
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Refine LS restraints |
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LS refinement shell |
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