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Yorodumi- PDB-5x4s: Structure of the N-terminal domain (NTD)of SARS-CoV spike protein -
+Open data
-Basic information
Entry | Database: PDB / ID: 5x4s | |||||||||
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Title | Structure of the N-terminal domain (NTD)of SARS-CoV spike protein | |||||||||
Components | Spike glycoprotein | |||||||||
Keywords | VIRAL PROTEIN / SARS-CoV / spike / N-terminal domain | |||||||||
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 | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.2 Å | |||||||||
Authors | Yuan, Y. / Zhang, Y. / Qi, J. / Shi, Y. / Gao, G.F. | |||||||||
Citation | Journal: Nat Commun / Year: 2017 Title: Cryo-EM structures of MERS-CoV and SARS-CoV spike glycoproteins reveal the dynamic receptor binding domains. Authors: Yuan Yuan / Duanfang Cao / Yanfang Zhang / Jun Ma / Jianxun Qi / Qihui Wang / Guangwen Lu / Ying Wu / Jinghua Yan / Yi Shi / Xinzheng Zhang / George F Gao / Abstract: The envelope spike (S) proteins of MERS-CoV and SARS-CoV determine the virus host tropism and entry into host cells, and constitute a promising target for the development of prophylactics and ...The envelope spike (S) proteins of MERS-CoV and SARS-CoV determine the virus host tropism and entry into host cells, and constitute a promising target for the development of prophylactics and therapeutics. Here, we present high-resolution structures of the trimeric MERS-CoV and SARS-CoV S proteins in its pre-fusion conformation by single particle cryo-electron microscopy. The overall structures resemble that from other coronaviruses including HKU1, MHV and NL63 reported recently, with the exception of the receptor binding domain (RBD). We captured two states of the RBD with receptor binding region either buried (lying state) or exposed (standing state), demonstrating an inherently flexible RBD readily recognized by the receptor. Further sequence conservation analysis of six human-infecting coronaviruses revealed that the fusion peptide, HR1 region and the central helix are potential targets for eliciting broadly neutralizing antibodies. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5x4s.cif.gz | 123.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5x4s.ent.gz | 97.9 KB | Display | PDB format |
PDBx/mmJSON format | 5x4s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5x4s_validation.pdf.gz | 793.4 KB | Display | wwPDB validaton report |
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Full document | 5x4s_full_validation.pdf.gz | 797.7 KB | Display | |
Data in XML | 5x4s_validation.xml.gz | 13.2 KB | Display | |
Data in CIF | 5x4s_validation.cif.gz | 17.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x4/5x4s ftp://data.pdbj.org/pub/pdb/validation_reports/x4/5x4s | HTTPS FTP |
-Related structure data
Related structure data | 6703C 6704C 6705C 6706C 6707C 5x4rC 5x58C 5x59C 5x5bC 5x5cC 5x5fC 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 32395.363 Da / Num. of mol.: 1 / Fragment: UNP residues 14-292 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human SARS coronavirus / Strain: BJ01 / Gene: S, 2 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P59594 |
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#2: 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 |
#3: Sugar | ChemComp-NAG / |
#4: Water | ChemComp-HOH / |
Sequence details | be based on strain, BJ01 |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.82 Å3/Da / Density % sol: 56.41 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 1.3 M Na/K hydrogen phosphate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1.039 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 21, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.039 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50 Å / Num. obs: 20329 / % possible obs: 99.4 % / Redundancy: 11.1 % / Net I/σ(I): 14.6 |
Reflection shell | Resolution: 2.2→2.28 Å / Redundancy: 14.2 % / Mean I/σ(I) obs: 5.9 / Num. unique obs: 1980 / % possible all: 100 |
-Processing
Software |
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Refinement | Resolution: 2.2→38.312 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 28.94 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→38.312 Å
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Refine LS restraints |
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LS refinement shell |
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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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