+Open data
-Basic information
Entry | Database: PDB / ID: 5vyh | ||||||
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Title | Crystal Structure of MERS-CoV S1 N-terminal Domain | ||||||
Components | S protein | ||||||
Keywords | VIRAL PROTEIN / fusion glycoprotein / virus | ||||||
Function / homology | Function and homology information : / endocytosis involved in viral entry into host cell / membrane => GO:0016020 / 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 / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope ...: / endocytosis involved in viral entry into host cell / membrane => GO:0016020 / 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 / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / host cell plasma membrane / virion membrane / membrane Similarity search - Function | ||||||
Biological species | Middle East respiratory syndrome-related coronavirus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Wang, N. / Wrapp, D. / Pallesen, J. / Ward, A.B. / McLellan, J.S. | ||||||
Funding support | United States, 1items
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Citation | Journal: Proc Natl Acad Sci U S A / Year: 2017 Title: Immunogenicity and structures of a rationally designed prefusion MERS-CoV spike antigen. Authors: Jesper Pallesen / Nianshuang Wang / Kizzmekia S Corbett / Daniel Wrapp / Robert N Kirchdoerfer / Hannah L Turner / Christopher A Cottrell / Michelle M Becker / Lingshu Wang / Wei Shi / Wing- ...Authors: Jesper Pallesen / Nianshuang Wang / Kizzmekia S Corbett / Daniel Wrapp / Robert N Kirchdoerfer / Hannah L Turner / Christopher A Cottrell / Michelle M Becker / Lingshu Wang / Wei Shi / Wing-Pui Kong / Erica L Andres / Arminja N Kettenbach / Mark R Denison / James D Chappell / Barney S Graham / Andrew B Ward / Jason S McLellan / Abstract: Middle East respiratory syndrome coronavirus (MERS-CoV) is a lineage C betacoronavirus that since its emergence in 2012 has caused outbreaks in human populations with case-fatality rates of ∼36%. ...Middle East respiratory syndrome coronavirus (MERS-CoV) is a lineage C betacoronavirus that since its emergence in 2012 has caused outbreaks in human populations with case-fatality rates of ∼36%. As in other coronaviruses, the spike (S) glycoprotein of MERS-CoV mediates receptor recognition and membrane fusion and is the primary target of the humoral immune response during infection. Here we use structure-based design to develop a generalizable strategy for retaining coronavirus S proteins in the antigenically optimal prefusion conformation and demonstrate that our engineered immunogen is able to elicit high neutralizing antibody titers against MERS-CoV. We also determined high-resolution structures of the trimeric MERS-CoV S ectodomain in complex with G4, a stem-directed neutralizing antibody. The structures reveal that G4 recognizes a glycosylated loop that is variable among coronaviruses and they define four conformational states of the trimer wherein each receptor-binding domain is either tightly packed at the membrane-distal apex or rotated into a receptor-accessible conformation. Our studies suggest a potential mechanism for fusion initiation through sequential receptor-binding events and provide a foundation for the structure-based design of coronavirus vaccines. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5vyh.cif.gz | 165.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5vyh.ent.gz | 129.9 KB | Display | PDB format |
PDBx/mmJSON format | 5vyh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5vyh_validation.pdf.gz | 701.2 KB | Display | wwPDB validaton report |
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Full document | 5vyh_full_validation.pdf.gz | 702.7 KB | Display | |
Data in XML | 5vyh_validation.xml.gz | 19.5 KB | Display | |
Data in CIF | 5vyh_validation.cif.gz | 29.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vy/5vyh ftp://data.pdbj.org/pub/pdb/validation_reports/vy/5vyh | HTTPS FTP |
-Related structure data
Related structure data | 8783C 8784C 8785C 8786C 8787C 8788C 8789C 8790C 8791C 8792C 8793C 5vzrC 5w9hC 5w9iC 5w9jC 5w9kC 5w9lC 5w9mC 5w9nC 5w9oC 5w9pC 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 / Sugars , 2 types, 9 molecules A
#1: Protein | Mass: 38511.090 Da / Num. of mol.: 1 / Fragment: N-terminal Domain (UNP residues 18-353) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Middle East respiratory syndrome-related coronavirus Plasmid: paH / Cell line (production host): HEK293F / Production host: Homo sapiens (human) / References: UniProt: T2B999, UniProt: K9N5Q8*PLUS |
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#2: Sugar | ChemComp-NAG / |
-Non-polymers , 4 types, 414 molecules
#3: Chemical | ChemComp-FOL / |
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#4: Chemical | ChemComp-MPD / ( |
#5: Chemical | ChemComp-IMD / |
#6: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.95 Å3/Da / Density % sol: 58.24 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 6.6%(w/v) PEG 8000, 0.99%(v/v) MPD, 0.1M Imidazole/ Hydrochloric acid pH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 1.18076 Å |
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Dec 3, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.18076 Å / Relative weight: 1 |
Reflection | Resolution: 2→54 Å / Num. obs: 31311 / % possible obs: 99.3 % / Redundancy: 6.9 % / CC1/2: 0.985 / Rmerge(I) obs: 0.186 / Rpim(I) all: 0.075 / Rrim(I) all: 0.201 / Net I/σ(I): 6.1 / Num. measured all: 216171 / Scaling rejects: 500 |
Reflection shell | Resolution: 2→2.05 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.7 / CC1/2: 0.731 / Rpim(I) all: 0.325 / Rrim(I) all: 0.777 / % possible all: 92.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: EM density Resolution: 2→45.482 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.86
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 75.33 Å2 / Biso mean: 27.7703 Å2 / Biso min: 5.55 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2→45.482 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 11
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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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