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Yorodumi- PDB-5xjk: NMR Structure and Localization of a Large Fragment of the SARS-Co... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5xjk | ||||||
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Title | NMR Structure and Localization of a Large Fragment of the SARS-CoV Fusion Protein: Implications in Viral Cell Fusion | ||||||
Components | Spike protein S2 | ||||||
Keywords | VIRAL PROTEIN | ||||||
Function / homology | Function and homology information Maturation of spike protein / Translation of Structural Proteins / Virion Assembly and Release / Attachment and Entry / endocytosis involved in viral entry into host cell / SARS-CoV-1 activates/modulates innate immune responses / suppression by virus of host tetherin activity / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / membrane fusion / positive regulation of viral entry into host cell ...Maturation of spike protein / Translation of Structural Proteins / Virion Assembly and Release / Attachment and Entry / endocytosis involved in viral entry into host cell / SARS-CoV-1 activates/modulates innate immune responses / suppression by virus of host tetherin activity / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / membrane fusion / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / symbiont-mediated suppression of host innate immune response / host cell surface receptor binding / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / host cell plasma membrane / virion membrane / identical protein binding / membrane Similarity search - Function | ||||||
Biological species | Human SARS coronavirus | ||||||
Method | SOLUTION NMR / torsion angle dynamics | ||||||
Authors | Bhattacharjya, S. / Chatterjee, D. | ||||||
Citation | Journal: Biochim. Biophys. Acta / Year: 2017 Title: NMR structure and localization of a large fragment of the SARS-CoV fusion protein: Implications in viral cell fusion. Authors: Mahajan, M. / Chatterjee, D. / Bhuvaneswari, K. / Pillay, S. / Bhattacharjya, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5xjk.cif.gz | 485.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5xjk.ent.gz | 420 KB | Display | PDB format |
PDBx/mmJSON format | 5xjk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5xjk_validation.pdf.gz | 470.7 KB | Display | wwPDB validaton report |
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Full document | 5xjk_full_validation.pdf.gz | 687 KB | Display | |
Data in XML | 5xjk_validation.xml.gz | 48.5 KB | Display | |
Data in CIF | 5xjk_validation.cif.gz | 49.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xj/5xjk ftp://data.pdbj.org/pub/pdb/validation_reports/xj/5xjk | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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NMR ensembles |
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-Components
#1: Protein | Mass: 7544.744 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 758-821 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human SARS coronavirus / Gene: S, 2 / Production host: Escherichia coli (E. coli) / References: UniProt: P59594 |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details | Type: micelle Contents: 0.2 M [U-13C; U-15N] Large Fragment of the SARS-CoV Fusion Protein, 90% H2O/10% D2O Label: 15 and 13C labeled / Solvent system: 90% H2O/10% D2O |
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Sample | Conc.: 0.2 M / Component: Large Fragment of the SARS-CoV Fusion Protein / Isotopic labeling: [U-13C; U-15N] |
Sample conditions | Ionic strength: 50 mM / Label: Uniformaly Double label / pH: 6.5 / Pressure: 1 atm / Temperature: 298 K |
-NMR measurement
NMR spectrometer | Type: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 600 MHz |
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-Processing
NMR software |
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Refinement | Method: torsion angle dynamics / Software ordinal: 2 | ||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 200 / Conformers submitted total number: 20 |