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Yorodumi- PDB-6xy2: Crystal structure of CTLA-4 complexed with the Fab of HL32 antibody -
+Open data
-Basic information
Entry | Database: PDB / ID: 6xy2 | ||||||
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Title | Crystal structure of CTLA-4 complexed with the Fab of HL32 antibody | ||||||
Components |
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Keywords | IMMUNE SYSTEM / CTLA-4 / Fab / antibody / immunnotherapy | ||||||
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 | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.05 Å | ||||||
Authors | Gao, H. / Zhou, A. | ||||||
Funding support | China, 1items
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Citation | Journal: Cell Discov / Year: 2020 Title: Structure of CTLA-4 complexed with a pH-sensitive cancer immunotherapeutic antibody. Authors: Gao, H. / Cai, H. / Liu, J. / Wang, X. / Zheng, P. / Devenport, M. / Xu, T. / Dou, F. / Liu, Y. / Zhou, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6xy2.cif.gz | 373.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6xy2.ent.gz | 261.1 KB | Display | PDB format |
PDBx/mmJSON format | 6xy2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xy/6xy2 ftp://data.pdbj.org/pub/pdb/validation_reports/xy/6xy2 | HTTPS FTP |
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-Related structure data
Related structure data | 3oskS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 13194.995 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CTLA4, CD152 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: P16410 |
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#2: Antibody | Mass: 26582.570 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293 / Production host: Homo sapiens (human) |
#3: Antibody | Mass: 23505.047 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293 / Production host: Homo sapiens (human) |
#4: Sugar | ChemComp-NAG / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 5.5 Å3/Da / Density % sol: 77.62 % |
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Crystal grow | Temperature: 293 K / Method: batch mode / pH: 6.5 / Details: 1M Li2SO4, 1.5M NH4SO4, 0.1M Sodium citrate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97892 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jan 13, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97892 Å / Relative weight: 1 |
Reflection | Resolution: 2.95→85 Å / Num. obs: 29874 / % possible obs: 99.9 % / Redundancy: 7.9 % / Biso Wilson estimate: 100.72 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.133 / Rpim(I) all: 0.049 / Rrim(I) all: 0.142 / Net I/σ(I): 7.4 |
Reflection shell | Resolution: 2.95→3.11 Å / Rmerge(I) obs: 1.865 / Mean I/σ(I) obs: 0.7 / Num. unique obs: 4226 / CC1/2: 0.372 / Rpim(I) all: 0.772 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3OSK Resolution: 3.05→75.33 Å / SU ML: 0.5355 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 35.7336 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: 70 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.05→75.33 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 28.2864927151 Å / Origin y: 32.5358881788 Å / Origin z: -10.0469404765 Å
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Refinement TLS group | Selection details: all |