[English] 日本語
Yorodumi- PDB-8hit: Crystal structure of anti-CTLA-4 humanized IgG1 MAb--JS007 in com... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8hit | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of anti-CTLA-4 humanized IgG1 MAb--JS007 in complex with human CTLA-4 | ||||||
Components |
| ||||||
Keywords | IMMUNE SYSTEM / complex / anti-body / ScFv | ||||||
Function / homology | Function and homology information 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 / adaptive immune response ...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 / adaptive immune response / immune response / positive regulation of apoptotic process / external side of plasma membrane / DNA damage response / perinuclear region of cytoplasm / Golgi apparatus / plasma membrane Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å | ||||||
Authors | Tan, S. / Shi, Y. / Wang, Q. / Gao, G.F. / Guan, J. / Chai, Y. / Qi, J. | ||||||
Funding support | China, 1items
| ||||||
Citation | Journal: Mabs / Year: 2023 Title: Characterization of the high-affinity anti-CTLA-4 monoclonal antibody JS007 for immune checkpoint therapy of cancer. Authors: Guan, J. / Liu, H. / Chai, Y. / Yu, J. / Yao, J. / Wang, J. / Pan, Z. / Zhang, J. / Zhou, Y. / Liu, H. / Yao, S. / Qi, J. / Feng, H. / Gao, G.F. / Wang, Q. / Shi, Y. / Tan, S. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 8hit.cif.gz | 80.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb8hit.ent.gz | 57 KB | Display | PDB format |
PDBx/mmJSON format | 8hit.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hi/8hit ftp://data.pdbj.org/pub/pdb/validation_reports/hi/8hit | HTTPS FTP |
---|
-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
---|
-Links
-Assembly
Deposited unit |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
Unit cell |
|
-Components
#1: Antibody | Mass: 13101.389 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli) |
---|---|
#2: Antibody | Mass: 11700.006 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli) |
#3: Protein | Mass: 12869.745 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CTLA4, CD152 / Production host: Escherichia coli (E. coli) / References: UniProt: P16410 |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.92 Å3/Da / Density % sol: 57.87 % |
---|---|
Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / Details: 100mM Tris, pH 8.5, 30% w/v PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97915 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 15, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97915 Å / Relative weight: 1 |
Reflection | Resolution: 3.2→50 Å / Num. obs: 7627 / % possible obs: 99.9 % / Redundancy: 15 % / Biso Wilson estimate: 59.21 Å2 / Rmerge(I) obs: 0.203 / Net I/σ(I): 15.4 |
Reflection shell | Resolution: 3.2→3.31 Å / Redundancy: 15.4 % / Mean I/σ(I) obs: 2.25 / Num. unique obs: 7627 / CC1/2: 0.826 / % possible all: 100 |
-Processing
Software |
| ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.2→45.58 Å / SU ML: -0 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.7524 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
| ||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||
Displacement parameters | Biso mean: 49.53 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.2→45.58 Å
| ||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||
LS refinement shell |
|