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Yorodumi- PDB-7ymz: Cryo-EM structure of MERS-CoV spike protein, intermediate conformation -
+Open data
-Basic information
Entry | Database: PDB / ID: 7ymz | ||||||
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Title | Cryo-EM structure of MERS-CoV spike protein, intermediate conformation | ||||||
Components | Spike glycoprotein | ||||||
Keywords | VIRAL PROTEIN / MERS-CoV / Spike / Glycoprotein | ||||||
Function / homology | Function and homology information host cell endoplasmic reticulum-Golgi intermediate compartment membrane / receptor-mediated endocytosis of virus by host cell / membrane fusion / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / symbiont entry into host cell / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / host cell plasma membrane ...host cell endoplasmic reticulum-Golgi intermediate compartment membrane / receptor-mediated endocytosis of virus by host cell / membrane fusion / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / symbiont entry into 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 | Human betacoronavirus 2c EMC/2012 | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.39 Å | ||||||
Authors | Hsu, S.T.D. / Chang, N.E. / Weng, Z.W. / Yang, T.J. / Draczkowski, P. | ||||||
Funding support | Taiwan, 1items
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Citation | Journal: To Be Published Title: GlycoSHIELD: a versatile pipeline to assess glycan impact on protein structures Authors: Gecht, M. / von Bulow, S. / Penet, C. / Hummer, G. / Hanus, C. / Sikora, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7ymz.cif.gz | 632.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7ymz.ent.gz | 513.6 KB | Display | PDB format |
PDBx/mmJSON format | 7ymz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7ymz_validation.pdf.gz | 2.4 MB | Display | wwPDB validaton report |
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Full document | 7ymz_full_validation.pdf.gz | 2.5 MB | Display | |
Data in XML | 7ymz_validation.xml.gz | 99.7 KB | Display | |
Data in CIF | 7ymz_validation.cif.gz | 155.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ym/7ymz ftp://data.pdbj.org/pub/pdb/validation_reports/ym/7ymz | HTTPS FTP |
-Related structure data
Related structure data | 33948MC 7ymtC 7ymvC 7ymwC 7ymxC 7ymyC 7yn0C M: map data used to model this data 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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-Components
#1: Protein | Mass: 150654.438 Da / Num. of mol.: 3 / Mutation: R748A, R751G, V1060P, L1061P Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human betacoronavirus 2c EMC/2012 / Production host: Homo sapiens (human) / References: UniProt: K0BRG7 #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: Polysaccharide | Source method: isolated from a genetically manipulated source #4: Polysaccharide | alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source #5: Sugar | ChemComp-NAG / Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: recombinant MERS-CoV (betacoronavirus 2c EMC 2012) fm2P Spike Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: #1 / Source: RECOMBINANT | ||||||||||||||||||||
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Molecular weight | Experimental value: NO | ||||||||||||||||||||
Source (natural) | Organism: Human betacoronavirus 2c EMC/2012 | ||||||||||||||||||||
Source (recombinant) | Organism: Homo sapiens (human) / Cell: Expi293F | ||||||||||||||||||||
Buffer solution | pH: 7.6 | ||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 0.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K Details: blot for 2.5 seconds before plunging; blot force: -1; waiting time: 30s. |
-Electron microscopy imaging
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |
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Microscopy | Model: FEI TALOS ARCTICA |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 92000 X / Nominal defocus max: 1700 nm / Nominal defocus min: 1500 nm |
Image recording | Electron dose: 40.6 e/Å2 / Film or detector model: FEI FALCON III (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 2886 |
-Processing
Software | Name: UCSF ChimeraX / Version: 1.2/v9 / Classification: model building / URL: https://www.rbvi.ucsf.edu/chimerax/ / Os: Windows / Type: package | ||||||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 1679870 | ||||||||||||||||||||||||||||
3D reconstruction | Resolution: 4.39 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 58940 / Symmetry type: POINT | ||||||||||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT / Space: REAL |