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- PDB-7k5l: Ebola virus VP40 octameric ring generated by an RNA oligonucleotide -
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Open data
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Basic information
Entry | Database: PDB / ID: 7k5l | ||||||
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Title | Ebola virus VP40 octameric ring generated by an RNA oligonucleotide | ||||||
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![]() | VIRAL PROTEIN / Ebola virus / transformer protein / RNA binding protein / matrix protein | ||||||
Function / homology | ![]() intracellular transport of virus / host cell endomembrane system / symbiont-mediated suppression of host defenses / symbiont-mediated suppression of host RNAi-mediated antiviral immune response / viral budding / host cell late endosome membrane / viral budding via host ESCRT complex / host cell membrane / viral budding from plasma membrane / host cell ...intracellular transport of virus / host cell endomembrane system / symbiont-mediated suppression of host defenses / symbiont-mediated suppression of host RNAi-mediated antiviral immune response / viral budding / host cell late endosome membrane / viral budding via host ESCRT complex / host cell membrane / viral budding from plasma membrane / host cell / structural constituent of virion / ribonucleoprotein complex / membrane raft / virus-mediated perturbation of host defense response / host cell plasma membrane / virion membrane / RNA binding / extracellular region / identical protein binding Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Landeras-Bueno, S. / Wasserman, H. / Salie, Z.L. / Saphire, E.O. | ||||||
![]() | ![]() Title: Cellular mRNA triggers structural transformation of Ebola virus matrix protein VP40 to its essential regulatory form. Authors: Landeras-Bueno, S. / Wasserman, H. / Oliveira, G. / VanAernum, Z.L. / Busch, F. / Salie, Z.L. / Wysocki, V.H. / Andersen, K. / Saphire, E.O. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 54.5 KB | Display | ![]() |
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PDB format | ![]() | 28.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 437.8 KB | Display | ![]() |
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Full document | ![]() | 437.8 KB | Display | |
Data in XML | ![]() | 7.8 KB | Display | |
Data in CIF | ![]() | 10.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7k5dC ![]() 4ldmS 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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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 19117.787 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: RNA chain | Mass: 11056.526 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.4 Details: 1 uL 3.5 mg/mL protein, 1 uL 75 mM sodium citrate tribasic pH 8.4, 150 mM ammonium acetate |
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-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 17, 2019 |
Radiation | Monochromator: CRYSTAL SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97931 Å / Relative weight: 1 |
Reflection | Resolution: 1.38→80.63 Å / Num. obs: 30977 / % possible obs: 95.7 % / Redundancy: 24.8 % / Biso Wilson estimate: 18.79 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.059 / Net I/σ(I): 27.8 |
Reflection shell | Resolution: 1.38→1.41 Å / Redundancy: 25.7 % / Rmerge(I) obs: 1.519 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 1580 / CC1/2: 0.853 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4LDM Resolution: 1.38→23.54 Å / SU ML: 0.1347 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.3609 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.21 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.38→23.54 Å
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Refine LS restraints |
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LS refinement shell |
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