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Yorodumi- PDB-7vpp: Structures of a deltacoronavirus spike protein bound to porcine a... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7vpp | ||||||
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Title | Structures of a deltacoronavirus spike protein bound to porcine and human receptors indicate the risk of virus adaptation to humans | ||||||
Components |
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Keywords | HYDROLASE/VIRAL PROTEIN / Porcine Deltacoronavirus / receptor / cross-species transmission / VIRAL PROTEIN / HYDROLASE-VIRAL PROTEIN complex | ||||||
Function / homology | Function and homology information Hydrolases; Acting on peptide bonds (peptidases); Aminopeptidases / peptide catabolic process / metalloaminopeptidase activity / host cell membrane / peptide binding / endocytosis involved in viral entry into host cell / regulation of blood pressure / membrane => GO:0016020 / receptor-mediated virion attachment to host cell / fusion of virus membrane with host plasma membrane ...Hydrolases; Acting on peptide bonds (peptidases); Aminopeptidases / peptide catabolic process / metalloaminopeptidase activity / host cell membrane / peptide binding / endocytosis involved in viral entry into host cell / regulation of blood pressure / membrane => GO:0016020 / receptor-mediated virion attachment to host cell / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion membrane / signal transduction / proteolysis / zinc ion binding / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Sus scrofa (pig) Porcine deltacoronavirus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.69 Å | ||||||
Authors | Ji, W. / Xu, Y. / Zhang, S. | ||||||
Funding support | China, 1items
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Citation | Journal: Nat Commun / Year: 2022 Title: Structures of a deltacoronavirus spike protein bound to porcine and human receptors. Authors: Ji, W. / Peng, Q. / Fang, X. / Li, Z. / Li, Y. / Xu, C. / Zhao, S. / Li, J. / Chen, R. / Mo, G. / Wei, Z. / Xu, Y. / Li, B. / Zhang, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7vpp.cif.gz | 400.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7vpp.ent.gz | 319.3 KB | Display | PDB format |
PDBx/mmJSON format | 7vpp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vp/7vpp ftp://data.pdbj.org/pub/pdb/validation_reports/vp/7vpp | HTTPS FTP |
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-Related structure data
Related structure data | 7vpqC 6atkS S: Starting model for refinement C: citing same article (ref.) |
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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
-Protein , 2 types, 3 molecules ACB
#1: Protein | Mass: 103803.555 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sus scrofa (pig) / Gene: ANPEP, pAPN / Production host: Baculovirus expression vector pFastBac1-HM References: UniProt: K7GMF9, Hydrolases; Acting on peptide bonds (peptidases); Aminopeptidases #2: Protein | | Mass: 14326.173 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Porcine deltacoronavirus / Production host: Baculovirus expression vector pFastBac1-HM / References: UniProt: A0A4P8D758 |
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-Sugars , 3 types, 15 molecules
#3: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source #4: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #7: Sugar | ChemComp-NAG / |
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-Non-polymers , 3 types, 42 molecules
#5: Chemical | #6: Chemical | ChemComp-GOL / #8: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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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: 3.41 Å3/Da / Density % sol: 63.93 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, hanging drop Details: solution containing 8% w/v Polyethylene glycol 1000, 8% w/v Polyethylene glycol 8000 and 20% w/v Glycerol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.979183 Å |
Detector | Type: DECTRIS PILATUS 12M / Detector: PIXEL / Date: Jun 20, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979183 Å / Relative weight: 1 |
Reflection | Resolution: 2.69→50 Å / Num. obs: 84784 / % possible obs: 99.2 % / Redundancy: 10.68 % / CC1/2: 0.997 / Net I/σ(I): 10.69 |
Reflection shell | Resolution: 2.69→2.85 Å / Num. unique obs: 12941 / CC1/2: 0.472 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6atk Resolution: 2.69→42.65 Å / SU ML: 0.42 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 23.35 / Stereochemistry target values: ML
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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 max: 174.85 Å2 / Biso mean: 65.5846 Å2 / Biso min: 28.97 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.69→42.65 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30
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