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- PDB-6w9y: De novo designed receptor transmembrane domains enhance CAR-T cyt... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6w9y | ||||||
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Title | De novo designed receptor transmembrane domains enhance CAR-T cytotoxicity and attenuate cytokine release | ||||||
![]() | De novo designed receptor transmembrane domain proMP 1.2 | ||||||
![]() | BIOSYNTHETIC PROTEIN / Transmembrane domain / de novo design | ||||||
Function / homology | (2S)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate![]() | ||||||
Biological species | synthetic construct (others) | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Call, M.J. / Call, M.E. / Chandler, N.J. / Nguyen, J.V. / Trenker, R. | ||||||
Funding support | ![]()
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![]() | ![]() Title: De novo designed receptor transmembrane domains enhance CAR-T cytotoxicity and attenuate cytokine release Authors: Elazar, A. / Chandler, N.J. / Davey, A.S. / Weinstein, J.Y. / Nguyen, J.V. / Trenker, R. / Jenkins, M. / Call, M.J. / Call, M.E. / Fleishman, S.J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 54.5 KB | Display | ![]() |
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PDB format | ![]() | 40.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 628.6 KB | Display | ![]() |
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Full document | ![]() | 629.2 KB | Display | |
Data in XML | ![]() | 5.9 KB | Display | |
Data in CIF | ![]() | 7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6w9zC ![]() 6wa0C ![]() 5eh6S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein/peptide | Mass: 3290.124 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Plasmid: pMM-TrpLE fusion / Production host: ![]() ![]() #2: Chemical | ChemComp-OLB / ( | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.21 Å3/Da / Density % sol: 44.38 % / Description: hexagonal discs |
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Crystal grow | Temperature: 293 K / Method: lipidic cubic phase / pH: 6 Details: 35 mg/ml peptide in LCP 25% w/v poly(ethylene glycol) 1500 10% v/v succinate-phosphate-glycine pH 6.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Ambient temp details: Cryo Stream / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 7, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.953737 Å / Relative weight: 1 |
Reflection | Resolution: 2.55→32.35 Å / Num. obs: 3956 / % possible obs: 98.94 % / Redundancy: 4.9 % / Biso Wilson estimate: 60.27 Å2 / CC1/2: 0.995 / CC star: 0.999 / Rmerge(I) obs: 0.06635 / Rpim(I) all: 0.0338 / Rrim(I) all: 0.07495 / Net I/σ(I): 12.72 |
Reflection shell | Resolution: 2.55→2.641 Å / Redundancy: 5 % / Rmerge(I) obs: 0.5728 / Mean I/σ(I) obs: 2.41 / Num. unique obs: 381 / CC1/2: 0.936 / CC star: 0.983 / Rpim(I) all: 0.2793 / Rrim(I) all: 0.6397 / % possible all: 97.14 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5EH6 Resolution: 2.55→32.35 Å / SU ML: 0.43 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 41.41
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 171.98 Å2 / Biso mean: 86.13 Å2 / Biso min: 41.72 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.55→32.35 Å
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LS refinement shell | Resolution: 2.55→2.641 Å
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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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