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- PDB-1h2c: Ebola virus matrix protein VP40 N-terminal domain in complex with... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1h2c | ||||||
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Title | Ebola virus matrix protein VP40 N-terminal domain in complex with RNA (High-resolution VP40[55-194] variant). | ||||||
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![]() | VIRUS/VIRAL PROTEIN / FILOVIRUS / EBOLA VIRUS / MATRIX PROTEIN VP40 / ASSEMBLY / BUDDING / VIRUS-VIRAL PROTEIN complex | ||||||
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 | ![]() ![]() ![]() | ||||||
![]() | Gomis-Ruth, F.X. / Dessen, A. / Bracher, A. / Klenk, H.D. / Weissenhorn, W. | ||||||
![]() | ![]() Title: The Matrix Protein Vp40 from Ebola Virus Octamerizes Into Pore-Like Structures with Specific RNA Binding Properties Authors: Gomis-Ruth, F.X. / Dessen, A. / Timmins, J. / Bracher, A. / Kolesnikowa, L. / Becker, S. / Klenk, H.D. / Weissenhorn, W. #1: ![]() Title: Crystal Structure of the Matrix Protein Vp40 from Ebola Virus Authors: Dessen, A. / Volchkov, V. / Dolnik, O. / Klenk, H.D. / Weissenhorn, W. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 43.2 KB | Display | ![]() |
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PDB format | ![]() | 28.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 447.6 KB | Display | ![]() |
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Full document | ![]() | 448.4 KB | Display | |
Data in XML | ![]() | 9 KB | Display | |
Data in CIF | ![]() | 12.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-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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Components on special symmetry positions |
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Details | BIOLOGICAL RELEVANT UNIT IS OCTAMERIC ASSOCIATIONOF THE PROTEIN SUBUNITS. |
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Components
#1: Protein | Mass: 15322.634 Da / Num. of mol.: 1 / Fragment: N-TERMINAL DOMAIN, RESIDUES 55-194 Source method: isolated from a genetically manipulated source Details: VP40[55-194] VARIANT / Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: RNA chain | Mass: 935.620 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: MRNA STOP CODON SEQUENCE, BIOCHEMICAL SYNTHESIS BY THE EXPRESSION HOST AND UPTAKE BY THE PROTEIN DURING OVEREXPRESSION Source: (natural) ![]() ![]() |
#3: Water | ChemComp-HOH / |
Compound details | THE BIOLOGICALLY RELEVANT OLIGOMER IS A HOMO-OCTAMER AS CREATED BY THE CRYSTALLOGRAPHIC 422 ...THE BIOLOGICAL |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 50 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 7.5 Details: 1 UL OF PROTEIN SOLUTION (10 MG/ML) AND 1 UL OF WELL SOLUTION (100 MM HEPES PH 7.5, 1.5 M NH4H2PO4,15 % MPD). HANGING DROP. | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.069 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→40 Å / Num. obs: 167556 / % possible obs: 95.9 % / Redundancy: 8.4 % / Rmerge(I) obs: 0.065 / Net I/σ(I): 7.1 |
Reflection | *PLUS Lowest resolution: 40 Å / Num. obs: 19961 / Num. measured all: 167556 |
Reflection shell | *PLUS % possible obs: 78.2 % / Redundancy: 2.9 % / Rmerge(I) obs: 0.341 / Mean I/σ(I) obs: 1.6 |
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Processing
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Refinement | Method to determine structure: ![]()
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Displacement parameters | Biso mean: 11.077 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→40 Å
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Refinement | *PLUS Lowest resolution: 40 Å | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
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