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Open data
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Basic information
Entry | Database: PDB / ID: 4ldd | ||||||
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Title | Crystal Structure of Ebola virus VP40 Hexamer | ||||||
![]() | Matrix protein VP40 | ||||||
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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 / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Bornholdt, Z.A. / Ableson, D.M. / Saphire, E.O. | ||||||
![]() | ![]() Title: Structural Rearrangement of Ebola Virus VP40 Begets Multiple Functions in the Virus Life Cycle. Authors: Bornholdt, Z.A. / Noda, T. / Abelson, D.M. / Halfmann, P. / Wood, M.R. / Kawaoka, Y. / 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 | ![]() | 110.9 KB | Display | ![]() |
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PDB format | ![]() | 84.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related 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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
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Components
#1: Protein | Mass: 32244.211 Da / Num. of mol.: 3 / Fragment: UNP residues 44-326 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.18 Å3/Da / Density % sol: 61.32 % |
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Crystal grow![]() | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.1 M bicine, 15% PEG20000, 3% dextran sulfate sodium salt (Mr = 5 kDa), pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K |
-Data collection
Diffraction | Mean temperature: 85 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 19, 2012 |
Radiation | Monochromator: Double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 3.497→136.087 Å / Num. all: 16369 / Num. obs: 16180 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 |
Reflection shell | Highest resolution: 3.497 Å |
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Processing
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Refinement | Method to determine structure![]() ![]()
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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: 3.498→44.885 Å
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Refine LS restraints |
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Refine LS restraints NCS |
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LS refinement shell |
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