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- PDB-5yzc: Crystal structure of the prefusion form of measles virus fusion p... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5yzc | ||||||||||||||||||
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Title | Crystal structure of the prefusion form of measles virus fusion protein in complex with a fusion inhibitor compound (AS-48) | ||||||||||||||||||
![]() | (glycoprotein ...) x 2 | ||||||||||||||||||
![]() | VIRAL PROTEIN / glycoprotein / fusion protein / paramyxovirus / inhibitor / chemical compound | ||||||||||||||||||
Function / homology | ![]() symbiont entry into host cell / fusion of virus membrane with host plasma membrane / viral envelope / host cell plasma membrane / virion membrane / membrane Similarity search - Function | ||||||||||||||||||
Biological species | ![]() | ||||||||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||||||||
![]() | Hashiguchi, T. / Fukuda, Y. / Matsuoka, R. / Kuroda, D. / Kubota, M. / Shirogane, Y. / Watanabe, S. / Tsumoto, K. / Kohda, D. / Plemper, R.K. / Yanagi, Y. | ||||||||||||||||||
Funding support | ![]() ![]()
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![]() | ![]() Title: Structures of the prefusion form of measles virus fusion protein in complex with inhibitors. Authors: Hashiguchi, T. / Fukuda, Y. / Matsuoka, R. / Kuroda, D. / Kubota, M. / Shirogane, Y. / Watanabe, S. / Tsumoto, K. / Kohda, D. / Plemper, R.K. / Yanagi, Y. | ||||||||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 108.1 KB | Display | ![]() |
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PDB format | ![]() | 79 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1 MB | Display | ![]() |
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Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 19.6 KB | Display | |
Data in CIF | ![]() | 27.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5yxwSC ![]() 5yzdC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components
-Glycoprotein ... , 2 types, 2 molecules AB
#1: Protein | Mass: 10524.273 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Protein | Mass: 44925.941 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: The fusion protein of glycoprotein F1,measles virus fusion protein and Tags Source: (gene. exp.) ![]() ![]() Strain: Ichinose-B95a, IC-B / Gene: F / Cell (production host): S2 / Production host: ![]() ![]() |
-Sugars , 2 types, 2 molecules ![](data/chem/img/NAG.gif)
#3: 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 |
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#4: Sugar | ChemComp-NAG / |
-Non-polymers , 2 types, 159 molecules ![](data/chem/img/95C.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/HOH.gif)
#5: Chemical | ChemComp-95C / |
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#6: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.66 Å3/Da / Density % sol: 66.38 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: sodium formate, glycerol, sodium acetate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Feb 23, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 2.334→119.852 Å / Num. obs: 34515 / % possible obs: 100 % / Redundancy: 20.9 % / Net I/σ(I): 14.3 |
Reflection shell | Resolution: 2.334→2.342 Å |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: 5YXW Resolution: 2.334→53.6 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.76 / 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: 2.334→53.6 Å
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Refine LS restraints |
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LS refinement shell |
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