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- PDB-1h2d: 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: 1h2d | ||||||
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Title | Ebola virus matrix protein VP40 N-terminal domain in complex with RNA (Low-resolution VP40[31-212] 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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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 69.9 KB | Display | ![]() |
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PDB format | ![]() | 50.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 462.8 KB | Display | ![]() |
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Full document | ![]() | 478 KB | Display | |
Data in XML | ![]() | 15.2 KB | Display | |
Data in CIF | ![]() | 20.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1h2cSC 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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Details | THE BIOLOGICALLY RELEVANT UNIT COMPRISES AN OCTAMEROF THE PROTEIN WHICH IS IN COMPLEX WITH RNA IN THISENTRY MAKING AN HEXADECAMER. SEE REMARK 400 BELOW |
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Components
#1: Protein | Mass: 19655.395 Da / Num. of mol.: 2 / Fragment: N-TERMINAL DOMAIN, RESIDUES 31-212 Source method: isolated from a genetically manipulated source Details: VP40[31-212] VARIANT / Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: RNA chain | Mass: 935.620 Da / Num. of mol.: 2 / 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: Chemical | #4: Water | ChemComp-HOH / | Compound details | THE BIOLOGICALLY RELEVANT OLIGOMER IS A HOMOOCTAMER AS CREATED BY THE CRYSTALLOGRAPHIC 222 SYMMETRY ...THE BIOLOGICAL | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.7 Å3/Da / Density % sol: 55 % / Description: PROTEIN DIMER USED AS SEARCH MODEL. | |||||||||||||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 4.6 Details: 1 UL OF PROTEIN (13 MG/ML) AND 1 UL OF WELL SOLUTION (100 MM NA-ACETATE PH4.6, 35 % MPD, 4 % GLYCEROL).HANGING DROP., pH 4.60 | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.5 / 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: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→60 Å / Num. obs: 63464 / % possible obs: 97.8 % / Redundancy: 4.4 % / Rmerge(I) obs: 0.085 / Net I/σ(I): 4.5 |
Reflection | *PLUS Lowest resolution: 60 Å / Num. obs: 14356 / Num. measured all: 63464 |
Reflection shell | *PLUS % possible obs: 86 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.406 / Mean I/σ(I) obs: 1.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1H2C Resolution: 2.6→60 Å / SU B: 17.547 / SU ML: 0.369 / Cross valid method: THROUGHOUT / ESU R: 0.568 / ESU R Free: 0.357 Details: 33% OF THE PROTEIN RESIDUES ARE DISORDERED, ACCOUNTING FOR VERY HIGH R-VALUES.
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Displacement parameters | Biso mean: 39.664 Å2
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Refinement step | Cycle: LAST / Resolution: 2.6→60 Å
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Refinement | *PLUS Lowest resolution: 59.8 Å | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
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