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- PDB-7jpi: Crystal structure of EBOV glycoprotein with modified HR2 stalk at... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7jpi | |||||||||
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Title | Crystal structure of EBOV glycoprotein with modified HR2 stalk at 2.3A resolution | |||||||||
![]() | (Envelope glycoprotein) x 2 | |||||||||
![]() | VIRAL PROTEIN / Ebola glycoprotein | |||||||||
Function / homology | ![]() host cell endoplasmic reticulum / viral budding from plasma membrane / clathrin-dependent endocytosis of virus by host cell / suppression by virus of host tetherin activity / host cell cytoplasm / entry receptor-mediated virion attachment to host cell / symbiont entry into host cell / membrane raft / fusion of virus membrane with host endosome membrane / viral envelope ...host cell endoplasmic reticulum / viral budding from plasma membrane / clathrin-dependent endocytosis of virus by host cell / suppression by virus of host tetherin activity / host cell cytoplasm / entry receptor-mediated virion attachment to host cell / symbiont entry into host cell / membrane raft / fusion of virus membrane with host endosome membrane / viral envelope / lipid binding / host cell plasma membrane / virion membrane / extracellular region / identical protein binding Similarity search - Function | |||||||||
Biological species | ![]() ![]() Zaire 1976 | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Chaudhary, A. / Stanfield, R.L. / Wilson, I.A. / Zhu, J. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Single-component multilayered self-assembling nanoparticles presenting rationally designed glycoprotein trimers as Ebola virus vaccines. Authors: He, L. / Chaudhary, A. / Lin, X. / Sou, C. / Alkutkar, T. / Kumar, S. / Ngo, T. / Kosviner, E. / Ozorowski, G. / Stanfield, R.L. / Ward, A.B. / Wilson, I.A. / Zhu, J. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 108.5 KB | Display | ![]() |
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PDB format | ![]() | 73.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.4 MB | Display | ![]() |
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Full document | ![]() | 1.4 MB | Display | |
Data in XML | ![]() | 17.6 KB | Display | |
Data in CIF | ![]() | 24.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7jphC ![]() 5jq3S 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
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 33246.555 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Protein | Mass: 18498.977 Da / Num. of mol.: 1 / Mutation: W615L Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
-Sugars , 3 types, 4 molecules ![](data/chem/img/NAG.gif)
#3: Polysaccharide | Source method: isolated from a genetically manipulated source #4: Polysaccharide | alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D- ...alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #6: Sugar | ChemComp-NAG / | |
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-Non-polymers , 3 types, 141 molecules ![](data/chem/img/GOL.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/HOH.gif)
#5: Chemical | #7: Chemical | ChemComp-PO4 / | #8: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | N |
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Sequence details | The complete sequence of chain A is IPLGVIHNSALQVSDVDKLVCRDKLSSTNQLRSVGLNLEGNGVATDVPSATKRWGFRSGV ...The complete sequence of chain A is IPLGVIHNSA |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.79 Å3/Da / Density meas: 74.31 Mg/m3 / Density % sol: 43.42 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: 0.M Sodium citrate, 10% PEG w/v 6000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 6, 2020 |
Radiation | Monochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.28→49.05 Å / Num. obs: 34904 / % possible obs: 96.4 % / Redundancy: 4.5 % / Biso Wilson estimate: 44.36 Å2 / CC1/2: 0.781 / Net I/σ(I): 8 |
Reflection shell | Resolution: 2.28→2.34 Å / Mean I/σ(I) obs: 0.9 / Num. unique obs: 1725 / CC1/2: 0.325 / % possible all: 97.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5JQ3 Resolution: 2.28→49 Å / SU ML: 0.3159 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.4449 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: 58.37 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.28→49 Å
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Refine LS restraints |
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LS refinement shell |
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