+Open data
-Basic information
Entry | Database: PDB / ID: 8p6q | ||||||||||||
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Title | Racemic structure of TNFR1 cysteine-rich domain | ||||||||||||
Components |
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Keywords | CYTOKINE / Racemic / Chemical Synthesis / Cysteine-rich / Cytokine Receptor / Receptor Mimic | ||||||||||||
Function / homology | Function and homology information positive regulation of amide metabolic process / tumor necrosis factor receptor superfamily complex / pulmonary valve development / aortic valve development / tumor necrosis factor receptor activity / positive regulation of lipid metabolic process / negative regulation of extracellular matrix constituent secretion / regulation of membrane lipid metabolic process / positive regulation of apoptotic process involved in morphogenesis / tumor necrosis factor binding ...positive regulation of amide metabolic process / tumor necrosis factor receptor superfamily complex / pulmonary valve development / aortic valve development / tumor necrosis factor receptor activity / positive regulation of lipid metabolic process / negative regulation of extracellular matrix constituent secretion / regulation of membrane lipid metabolic process / positive regulation of apoptotic process involved in morphogenesis / tumor necrosis factor binding / TNFs bind their physiological receptors / negative regulation of cardiac muscle hypertrophy / TNF signaling / TNFR1-mediated ceramide production / regulation of establishment of endothelial barrier / regulation of tumor necrosis factor-mediated signaling pathway / TNFR1-induced proapoptotic signaling / positive regulation of execution phase of apoptosis / prostaglandin metabolic process / Interleukin-10 signaling / extrinsic apoptotic signaling pathway via death domain receptors / positive regulation of tyrosine phosphorylation of STAT protein / tumor necrosis factor-mediated signaling pathway / TNFR1-induced NF-kappa-B signaling pathway / protein localization to plasma membrane / Regulation of TNFR1 signaling / negative regulation of inflammatory response / positive regulation of inflammatory response / cytokine-mediated signaling pathway / cellular response to mechanical stimulus / intrinsic apoptotic signaling pathway in response to DNA damage / positive regulation of canonical NF-kappaB signal transduction / transcription by RNA polymerase II / receptor complex / defense response to bacterium / inflammatory response / membrane raft / Golgi membrane / cell surface / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular region / membrane / plasma membrane Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å | ||||||||||||
Authors | Lander, A.J. / Jin, Y. / Luk, L.Y.P. | ||||||||||||
Funding support | United Kingdom, 3items
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Citation | Journal: Acs Bio Med Chem Au / Year: 2024 Title: Deciphering the Synthetic and Refolding Strategy of a Cysteine-Rich Domain in the Tumor Necrosis Factor Receptor (TNF-R) for Racemic Crystallography Analysis and d-Peptide Ligand Discovery. Authors: Lander, A.J. / Kong, Y. / Jin, Y. / Wu, C. / Luk, L.Y.P. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8p6q.cif.gz | 65.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8p6q.ent.gz | 47.8 KB | Display | PDB format |
PDBx/mmJSON format | 8p6q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p6/8p6q ftp://data.pdbj.org/pub/pdb/validation_reports/p6/8p6q | HTTPS FTP |
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-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein/peptide | Mass: 5349.054 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P19438 | ||||
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#2: Polypeptide(D) | Mass: 5346.033 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) | ||||
#3: Chemical | ChemComp-SO4 / #4: Water | ChemComp-HOH / | 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: 2.22 Å3/Da / Density % sol: 44.7 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 250 nL of DL-TNFR-1 CRD2 (25 mg/mL) and 250 nL of precipitant (1.5 M Sodium chloride, 10% v/v ethanol, pH 8.5) were mixed in the sitting drop. The single, block shaped crystal was dipped ...Details: 250 nL of DL-TNFR-1 CRD2 (25 mg/mL) and 250 nL of precipitant (1.5 M Sodium chloride, 10% v/v ethanol, pH 8.5) were mixed in the sitting drop. The single, block shaped crystal was dipped into 2.0 M lithium sulfate and flash frozen in liquid nitrogen during harvesting. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.6767 Å |
Detector | Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jul 24, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.6767 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→34.06 Å / Num. obs: 18553 / % possible obs: 100 % / Redundancy: 6.01 % / CC1/2: 0.999 / Net I/σ(I): 11.3 |
Reflection shell | Resolution: 1.4→1.42 Å / Mean I/σ(I) obs: 1 / Num. unique obs: 898 / CC1/2: 0.785 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.4→34.06 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.942 / SU B: 3.752 / SU ML: 0.065 / Cross valid method: FREE R-VALUE / ESU R: 0.093 / ESU R Free: 0.084 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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 mean: 14.739 Å2
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Refinement step | Cycle: 1 / Resolution: 1.4→34.06 Å
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