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- PDB-7dv4: Crystal structure of anti-CTLA-4 VH domain in complex with human ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7dv4 | ||||||
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Title | Crystal structure of anti-CTLA-4 VH domain in complex with human CTLA-4 | ||||||
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Function / homology | ![]() protein complex involved in cell adhesion / negative regulation of regulatory T cell differentiation / RUNX1 and FOXP3 control the development of regulatory T lymphocytes (Tregs) / clathrin-coated endocytic vesicle / CTLA4 inhibitory signaling / negative regulation of B cell proliferation / negative regulation of T cell proliferation / B cell receptor signaling pathway / T cell receptor signaling pathway / ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Li, H. / Gan, X. / He, Y. | ||||||
![]() | ![]() Title: An anti-CTLA-4 heavy chain-only antibody with enhanced T reg depletion shows excellent preclinical efficacy and safety profile. Authors: Gan, X. / Shan, Q. / Li, H. / Janssens, R. / Shen, Y. / He, Y. / Chen, F. / van Haperen, R. / Drabek, D. / Li, J. / Zhang, Y. / Zhao, J. / Qin, B. / Jheng, M.J. / Chen, V. / Wang, J. / Rong, Y. / Grosveld, F. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 186.2 KB | Display | ![]() |
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PDB format | ![]() | 148.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | ![]() Mass: 12669.487 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() #2: Antibody | Mass: 12891.441 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() #3: Chemical | ![]() #4: Water | ChemComp-HOH / | ![]() Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.74 Å3/Da / Density % sol: 55.05 % |
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Crystal grow![]() | Temperature: 291 K / Method: vapor diffusion, sitting drop / Details: 100 mM sodium citrate, 10% (w/v) PEG 6000, pH 5.0 |
-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: Apr 18, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.38→44.73 Å / Num. obs: 45646 / % possible obs: 99.8 % / Redundancy: 6.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.037 / Rpim(I) all: 0.016 / Rrim(I) all: 0.041 / Net I/σ(I): 23.5 / Num. measured all: 293482 / Scaling rejects: 58 |
Reflection shell | Resolution: 2.38→2.46 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.867 / Num. unique obs: 4411 / CC1/2: 0.693 / Rpim(I) all: 0.391 / Rrim(I) all: 0.953 / % possible all: 100 |
-Phasing
Phasing![]() | Method: ![]() |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 3OSK,5AZE Resolution: 2.38→42.33 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.944 / SU B: 10.917 / SU ML: 0.243 / Cross valid method: THROUGHOUT / ESU R: 0.373 / ESU R Free: 0.254 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 164.18 Å2 / Biso min: 41 Å2
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Refinement step | Cycle: final / Resolution: 2.38→42.33 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.38→2.442 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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