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- PDB-7yds: The structure of the bispecific antibody targeted PD-L1 and 4-1BB -
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Open data
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Basic information
Entry | Database: PDB / ID: 7yds | ||||||||||||
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Title | The structure of the bispecific antibody targeted PD-L1 and 4-1BB | ||||||||||||
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![]() | IMMUNE SYSTEM / Complex / Checkpoint inhibitors | ||||||||||||
Function / homology | ![]() positive regulation of tolerance induction to tumor cell / negative regulation of tumor necrosis factor superfamily cytokine production / positive regulation of activated CD8-positive, alpha-beta T cell apoptotic process / negative regulation of CD8-positive, alpha-beta T cell activation / TRIF-dependent toll-like receptor signaling pathway / negative regulation of CD4-positive, alpha-beta T cell proliferation / STAT3 nuclear events downstream of ALK signaling / negative regulation of interleukin-10 production / negative regulation of activated T cell proliferation / positive regulation of interleukin-10 production ...positive regulation of tolerance induction to tumor cell / negative regulation of tumor necrosis factor superfamily cytokine production / positive regulation of activated CD8-positive, alpha-beta T cell apoptotic process / negative regulation of CD8-positive, alpha-beta T cell activation / TRIF-dependent toll-like receptor signaling pathway / negative regulation of CD4-positive, alpha-beta T cell proliferation / STAT3 nuclear events downstream of ALK signaling / negative regulation of interleukin-10 production / negative regulation of activated T cell proliferation / positive regulation of interleukin-10 production / negative regulation of type II interferon production / PD-1 signaling / positive regulation of T cell proliferation / T cell costimulation / response to cytokine / recycling endosome membrane / actin cytoskeleton / early endosome membrane / cellular response to lipopolysaccharide / adaptive immune response / transcription coactivator activity / cell surface receptor signaling pathway / positive regulation of cell migration / immune response / external side of plasma membrane / signal transduction / extracellular exosome / nucleoplasm / plasma membrane Similarity search - Function | ||||||||||||
Biological species | ![]() | ||||||||||||
Method | ![]() ![]() | ||||||||||||
![]() | Gao, Y. / Zhu, M. / Liu, W.T. / Cheng, L.S. / Zhu, Z.L. / Niu, L.W. | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: A bispecific antibody targeted PD-L1 and 4-1BB induces a potent antitumor immune activity in colorectal cancer without systemic toxicity Authors: Zhu, M. / Gao, Y. | ||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 130.8 KB | Display | ![]() |
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PDB format | ![]() | 98.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 448.4 KB | Display | ![]() |
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Full document | ![]() | 451.9 KB | Display | |
Data in XML | ![]() | 24.9 KB | Display | |
Data in CIF | ![]() | 36.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3bisS ![]() 6wkmS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homology ![]() |
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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
#1: Protein | Mass: 17080.676 Da / Num. of mol.: 1 / Mutation: N35Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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#2: Antibody | Mass: 23386.199 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
#3: Antibody | Mass: 23725.256 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: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.36 Å3/Da / Density % sol: 47.87 % |
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Crystal grow | Temperature: 289.15 K / Method: vapor diffusion, sitting drop / Details: 18% PEG4000, 0.1M Bis-tris pH 6.2 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() |
Detector | Type: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Apr 9, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54056 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→13.14 Å / Num. obs: 29320 / % possible obs: 99.27 % / Redundancy: 2 % / Biso Wilson estimate: 24.45 Å2 / CC1/2: 0.983 / CC star: 0.996 / Rmerge(I) obs: 0.1091 / Rpim(I) all: 0.1091 / Rrim(I) all: 0.1544 / Net I/σ(I): 8.23 |
Reflection shell | Resolution: 2.3→2.382 Å / Redundancy: 2 % / Rmerge(I) obs: 0.5817 / Mean I/σ(I) obs: 1.29 / Num. unique obs: 2885 / CC1/2: 0.455 / CC star: 0.791 / Rpim(I) all: 0.5817 / Rrim(I) all: 0.8226 / % possible all: 99.55 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6WKM, 3BIS Resolution: 2.3→13.14 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.71 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 113.39 Å2 / Biso mean: 29.8084 Å2 / Biso min: 7.03 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.3→13.14 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10 / % reflection obs: 100 %
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