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Yorodumi- PDB-7ymx: Cryo-EM structure of MERS-CoV spike protein, One RBD-up conformation 2 -
+Open data
-Basic information
Entry | Database: PDB / ID: 7ymx | ||||||
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Title | Cryo-EM structure of MERS-CoV spike protein, One RBD-up conformation 2 | ||||||
Components | Spike glycoprotein | ||||||
Keywords | VIRAL PROTEIN / MERS-CoV / Spike / Glycoprotein | ||||||
Function / homology | Function and homology information host cell endoplasmic reticulum-Golgi intermediate compartment membrane / membrane fusion / receptor-mediated endocytosis of virus by host cell / 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 / membrane fusion / receptor-mediated endocytosis of virus by host cell / 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: 4.44 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: Cell / Year: 2024 Title: Rapid simulation of glycoprotein structures by grafting and steric exclusion of glycan conformer libraries. Authors: Yu-Xi Tsai / Ning-En Chang / Klaus Reuter / Hao-Ting Chang / Tzu-Jing Yang / Sören von Bülow / Vidhi Sehrawat / Noémie Zerrouki / Matthieu Tuffery / Michael Gecht / Isabell Louise ...Authors: Yu-Xi Tsai / Ning-En Chang / Klaus Reuter / Hao-Ting Chang / Tzu-Jing Yang / Sören von Bülow / Vidhi Sehrawat / Noémie Zerrouki / Matthieu Tuffery / Michael Gecht / Isabell Louise Grothaus / Lucio Colombi Ciacchi / Yong-Sheng Wang / Min-Feng Hsu / Kay-Hooi Khoo / Gerhard Hummer / Shang-Te Danny Hsu / Cyril Hanus / Mateusz Sikora / Abstract: Most membrane proteins are modified by covalent addition of complex sugars through N- and O-glycosylation. Unlike proteins, glycans do not typically adopt specific secondary structures and remain ...Most membrane proteins are modified by covalent addition of complex sugars through N- and O-glycosylation. Unlike proteins, glycans do not typically adopt specific secondary structures and remain very mobile, shielding potentially large fractions of protein surface. High glycan conformational freedom hinders complete structural elucidation of glycoproteins. Computer simulations may be used to model glycosylated proteins but require hundreds of thousands of computing hours on supercomputers, thus limiting routine use. Here, we describe GlycoSHIELD, a reductionist method that can be implemented on personal computers to graft realistic ensembles of glycan conformers onto static protein structures in minutes. Using molecular dynamics simulation, small-angle X-ray scattering, cryoelectron microscopy, and mass spectrometry, we show that this open-access toolkit provides enhanced models of glycoprotein structures. Focusing on N-cadherin, human coronavirus spike proteins, and gamma-aminobutyric acid receptors, we show that GlycoSHIELD can shed light on the impact of glycans on the conformation and activity of complex glycoproteins. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7ymx.cif.gz | 628.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7ymx.ent.gz | 510.4 KB | Display | PDB format |
PDBx/mmJSON format | 7ymx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7ymx_validation.pdf.gz | 2.1 MB | Display | wwPDB validaton report |
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Full document | 7ymx_full_validation.pdf.gz | 2.2 MB | Display | |
Data in XML | 7ymx_validation.xml.gz | 98.5 KB | Display | |
Data in CIF | 7ymx_validation.cif.gz | 154.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ym/7ymx ftp://data.pdbj.org/pub/pdb/validation_reports/ym/7ymx | HTTPS FTP |
-Related structure data
Related structure data | 33946MC 7ymtC 7ymvC 7ymwC 7ymyC 7ymzC 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: 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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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: 4.44 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 65063 / Symmetry type: POINT | ||||||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT / Space: REAL |