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Yorodumi- PDB-7sjq: Ex silico engineering of cystine-dense peptides yielding a potent... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7sjq | ||||||
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Title | Ex silico engineering of cystine-dense peptides yielding a potent bispecific T-cell engager | ||||||
Components |
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Keywords | ANTITUMOR PROTEIN / PDL1 binder | ||||||
Function / homology | Function and homology information 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 / negative regulation of T cell mediated immune response to tumor cell / 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 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 / negative regulation of T cell mediated immune response to tumor cell / 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 / receptor ligand activity / positive regulation of cell migration / immune response / external side of plasma membrane / signal transduction / extracellular exosome / nucleoplasm / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Rupert, P.B. / Strong, R. | ||||||
Funding support | 1items
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Citation | Journal: Sci Transl Med / Year: 2022 Title: Ex silico engineering of cystine-dense peptides yielding a potent bispecific T cell engager. Authors: Crook, Z.R. / Girard, E.J. / Sevilla, G.P. / Brusniak, M.Y. / Rupert, P.B. / Friend, D.J. / Gewe, M.M. / Clarke, M. / Lin, I. / Ruff, R. / Pakiam, F. / Phi, T.D. / Bandaranayake, A. / ...Authors: Crook, Z.R. / Girard, E.J. / Sevilla, G.P. / Brusniak, M.Y. / Rupert, P.B. / Friend, D.J. / Gewe, M.M. / Clarke, M. / Lin, I. / Ruff, R. / Pakiam, F. / Phi, T.D. / Bandaranayake, A. / Correnti, C.E. / Mhyre, A.J. / Nairn, N.W. / Strong, R.K. / Olson, J.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7sjq.cif.gz | 78.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7sjq.ent.gz | 55.8 KB | Display | PDB format |
PDBx/mmJSON format | 7sjq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sj/7sjq ftp://data.pdbj.org/pub/pdb/validation_reports/sj/7sjq | HTTPS FTP |
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-Related structure data
Related structure data | 7saoC 7sapC 7sgqC 7sltC 7sncC 7sndC 5c3tS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein , 2 types, 2 molecules AD
#1: Protein | Mass: 13538.503 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CD274, B7H1, PDCD1L1, PDCD1LG1, PDL1 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: Q9NZQ7 |
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#2: Protein | Mass: 5671.515 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
-Sugars , 1 types, 1 molecules
#4: Sugar | ChemComp-NAG / |
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-Non-polymers , 4 types, 80 molecules
#3: Chemical | ChemComp-GOL / |
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#5: Chemical | ChemComp-SO4 / |
#6: Chemical | ChemComp-NA / |
#7: Water | ChemComp-HOH / |
-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.38 Å3/Da / Density % sol: 48.32 % |
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Crystal grow | Temperature: 300 K / Method: vapor diffusion, hanging drop / Details: Sodium Citrate pH 7, ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: Sep 9, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→99.91 Å / Num. obs: 12762 / % possible obs: 99.8 % / Redundancy: 4.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.039 / Net I/σ(I): 32.45 |
Reflection shell | Resolution: 2→2.07 Å / Rmerge(I) obs: 0.154 / Mean I/σ(I) obs: 8.26 / Num. unique obs: 1278 / CC1/2: 0.968 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5C3T Resolution: 2→28.04 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.921 / SU B: 6.907 / SU ML: 0.098 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.167 / ESU R Free: 0.154 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
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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: 88.16 Å2 / Biso mean: 22.768 Å2 / Biso min: 9.95 Å2
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Refinement step | Cycle: final / Resolution: 2→28.04 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.052 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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