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- PDB-5f1b: Structural basis of Ebola virus entry: viral glycoprotein bound t... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5f1b | |||||||||
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Title | Structural basis of Ebola virus entry: viral glycoprotein bound to its endosomal receptor Niemann-Pick C1 | |||||||||
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![]() | VIRAL PROTEIN/TRANSPORT PROTEIN / Ebola virus / glycoprotein / NPC1-C / VIRAL PROTEIN-TRANSPORT PROTEIN complex | |||||||||
Function / homology | ![]() cyclodextrin metabolic process / cholesterol storage / membrane raft organization / : / intracellular cholesterol transport / intracellular lipid transport / intestinal cholesterol absorption / LDL clearance / negative regulation of epithelial cell apoptotic process / bile acid metabolic process ...cyclodextrin metabolic process / cholesterol storage / membrane raft organization / : / intracellular cholesterol transport / intracellular lipid transport / intestinal cholesterol absorption / LDL clearance / negative regulation of epithelial cell apoptotic process / bile acid metabolic process / cholesterol transport / programmed cell death / establishment of protein localization to membrane / adult walking behavior / lysosomal transport / cholesterol efflux / cellular response to steroid hormone stimulus / negative regulation of macroautophagy / cholesterol binding / protein glycosylation / cellular response to low-density lipoprotein particle stimulus / response to cadmium ion / negative regulation of TORC1 signaling / cholesterol metabolic process / neurogenesis / liver development / cholesterol homeostasis / macroautophagy / autophagy / endocytosis / transmembrane signaling receptor activity / late endosome membrane / nuclear envelope / virus receptor activity / signaling receptor activity / gene expression / clathrin-dependent endocytosis of virus by host cell / suppression by virus of host tetherin activity / entry receptor-mediated virion attachment to host cell / lysosome / response to xenobiotic stimulus / symbiont entry into host cell / membrane raft / lysosomal membrane / fusion of virus membrane with host endosome membrane / viral envelope / lipid binding / host cell plasma membrane / virion membrane / perinuclear region of cytoplasm / Golgi apparatus / endoplasmic reticulum / extracellular exosome / extracellular region / membrane / plasma membrane Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Wang, H. / Shi, Y. / Song, J. / Qi, J. / Lu, G. / Yan, J. / Gao, G.F. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Ebola Viral Glycoprotein Bound to Its Endosomal Receptor Niemann-Pick C1. Authors: Wang, H. / Shi, Y. / Song, J. / Qi, J. / Lu, G. / Yan, J. / Gao, G.F. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 205.5 KB | Display | ![]() |
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PDB format | ![]() | 162.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 772.5 KB | Display | ![]() |
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Full document | ![]() | 780.1 KB | Display | |
Data in XML | ![]() | 20.9 KB | Display | |
Data in CIF | ![]() | 29.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5f18C ![]() 3csyS C: citing same article ( S: Starting model for refinement |
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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
#1: Protein | Mass: 17194.543 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 32-188 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Protein | Mass: 14882.807 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 509-598 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
#3: Protein | Mass: 29436.582 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 374-620 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
#4: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.53 Å3/Da / Density % sol: 51.41 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 15% (v/v) pentaerythritolpropoxylate, 0.2M sodium chloride, pH 5.5, 0.1M MES-NaOH |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Jun 18, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→50 Å / Num. obs: 27329 / % possible obs: 100 % / Redundancy: 19.6 % / Net I/σ(I): 32.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3CSY Resolution: 2.3→41.858 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.61 / Stereochemistry target values: ML
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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: 2.3→41.858 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 30.2833 Å / Origin y: -16.3893 Å / Origin z: -320.9409 Å
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Refinement TLS group | Selection details: all |