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Yorodumi- PDB-8enx: Crystal structure of beta'-COPI-WD40 domain Y33A mutant in comple... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8enx | |||||||||
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Title | Crystal structure of beta'-COPI-WD40 domain Y33A mutant in complex with SARS-CoV-2 clientized spike tail heptapeptide. | |||||||||
Components |
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Keywords | PROTEIN TRANSPORT / COPI / protein trafficking / SARS-CoV-2 spike / dibasic motif | |||||||||
Function / homology | Function and homology information COPI vesicle coat / intra-Golgi vesicle-mediated transport / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / endoplasmic reticulum to Golgi vesicle-mediated transport / intracellular protein transport / Golgi membrane / structural molecule activity Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) Severe acute respiratory syndrome coronavirus 2 | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | |||||||||
Authors | Dey, D. / Hasan, S.S. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Nat Commun / Year: 2023 Title: A single C-terminal residue controls SARS-CoV-2 spike trafficking and incorporation into VLPs. Authors: Dey, D. / Qing, E. / He, Y. / Chen, Y. / Jennings, B. / Cohn, W. / Singh, S. / Gakhar, L. / Schnicker, N.J. / Pierce, B.G. / Whitelegge, J.P. / Doray, B. / Orban, J. / Gallagher, T. / Hasan, S.S. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8enx.cif.gz | 312.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8enx.ent.gz | 205.2 KB | Display | PDB format |
PDBx/mmJSON format | 8enx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8enx_validation.pdf.gz | 429.8 KB | Display | wwPDB validaton report |
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Full document | 8enx_full_validation.pdf.gz | 430.9 KB | Display | |
Data in XML | 8enx_validation.xml.gz | 30.7 KB | Display | |
Data in CIF | 8enx_validation.cif.gz | 48.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/en/8enx ftp://data.pdbj.org/pub/pdb/validation_reports/en/8enx | HTTPS FTP |
-Related structure data
Related structure data | 8ensC 8enwC 8enyC 8enzC 8eo0C 8szxC 4j79S 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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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 34288.633 Da / Num. of mol.: 2 / Mutation: Y33A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Production host: Escherichia coli (E. coli) / References: UniProt: G2WDW6 #2: Protein/peptide | | Mass: 846.970 Da / Num. of mol.: 1 / Source method: obtained synthetically Source: (synth.) Severe acute respiratory syndrome coronavirus 2 #3: Water | ChemComp-HOH / | |
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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: 2.21 Å3/Da / Density % sol: 44.35 % |
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Crystal grow | Temperature: 295.15 K / Method: vapor diffusion, hanging drop / pH: 6.2 / Details: 0.1M MES pH 6.2, 17% PEG20000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.92 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: May 17, 2022 / Details: KB bimorph mirrors |
Radiation | Monochromator: Si(111) DCM / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→28.33 Å / Num. obs: 53029 / % possible obs: 96.6 % / Redundancy: 2.4 % / Biso Wilson estimate: 16.09 Å2 / CC1/2: 0.989 / Rsym value: 0.137 / Net I/σ(I): 3.7 |
Reflection shell | Resolution: 1.8→1.84 Å / Mean I/σ(I) obs: 1 / Num. unique obs: 2959 / CC1/2: 0.551 / Rsym value: 0.713 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4J79 Resolution: 1.8→28.33 Å / SU ML: 0.2042 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 18.0525 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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 mean: 19.23 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→28.33 Å
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Refine LS restraints |
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LS refinement shell |
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