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Yorodumi- PDB-8d87: Fitted crystal structure of the homotrimer of fusion glycoprotein... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8d87 | |||||||||
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Title | Fitted crystal structure of the homotrimer of fusion glycoprotein E1 from SFV into subtomogram averaged CHIKV E1 glycoprotein density | |||||||||
Components | Spike glycoprotein E1 | |||||||||
Keywords | VIRAL PROTEIN / envelope glycoprotein / membrane fusion / virus | |||||||||
Function / homology | Function and homology information togavirin / T=4 icosahedral viral capsid / virion assembly / small molecule binding / host cell endosome / symbiont-mediated suppression of host toll-like receptor signaling pathway / clathrin-dependent endocytosis of virus by host cell / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / viral envelope ...togavirin / T=4 icosahedral viral capsid / virion assembly / small molecule binding / host cell endosome / symbiont-mediated suppression of host toll-like receptor signaling pathway / clathrin-dependent endocytosis of virus by host cell / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / viral envelope / host cell nucleus / virion attachment to host cell / host cell plasma membrane / virion membrane / structural molecule activity / proteolysis / RNA binding / membrane Similarity search - Function | |||||||||
Biological species | Chikungunya virus strain S27-African prototype | |||||||||
Method | ELECTRON MICROSCOPY / SYNCHROTRON / subtomogram averaging / MAD, MIR / cryo EM / Resolution: 27.2 Å | |||||||||
Authors | Mangala Prasad, V. / Lee, K.K. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Nat Commun / Year: 2022 Title: Visualization of conformational changes and membrane remodeling leading to genome delivery by viral class-II fusion machinery. Authors: Vidya Mangala Prasad / Jelle S Blijleven / Jolanda M Smit / Kelly K Lee / Abstract: Chikungunya virus (CHIKV) is a human pathogen that delivers its genome to the host cell cytoplasm through endocytic low pH-activated membrane fusion mediated by class-II fusion proteins. Though ...Chikungunya virus (CHIKV) is a human pathogen that delivers its genome to the host cell cytoplasm through endocytic low pH-activated membrane fusion mediated by class-II fusion proteins. Though structures of prefusion, icosahedral CHIKV are available, structural characterization of virion interaction with membranes has been limited. Here, we have used cryo-electron tomography to visualize CHIKV's complete membrane fusion pathway, identifying key intermediary glycoprotein conformations coupled to membrane remodeling events. Using sub-tomogram averaging, we elucidate features of the low pH-exposed virion, nucleocapsid and full-length E1-glycoprotein's post-fusion structure. Contrary to class-I fusion systems, CHIKV achieves membrane apposition by protrusion of extended E1-glycoprotein homotrimers into the target membrane. The fusion process also features a large hemifusion diaphragm that transitions to a wide pore for intact nucleocapsid delivery. Our analyses provide comprehensive ultrastructural insights into the class-II virus fusion system function and direct mechanistic characterization of the fundamental process of protein-mediated membrane fusion. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8d87.cif.gz | 243.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8d87.ent.gz | 194.7 KB | Display | PDB format |
PDBx/mmJSON format | 8d87.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d8/8d87 ftp://data.pdbj.org/pub/pdb/validation_reports/d8/8d87 | HTTPS FTP |
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-Related structure data
Related structure data | 27248MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Protein , 1 types, 3 molecules ABC
#1: Protein | Mass: 42690.125 Da / Num. of mol.: 3 / Fragment: SPIKE GLYCOPROTEIN E1 / Source method: isolated from a natural source Details: The previously determined X-ray crystal structure PDB ID 1RER was rigidly docked into the sub-tomogram averaged map but no further refinement was performed Source: (natural) Chikungunya virus strain S27-African prototype References: UniProt: P03315 |
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-Sugars , 3 types, 3 molecules
#2: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-beta-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4) ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-beta-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
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#3: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-alpha-D-glucopyranose Type: oligosaccharide / Mass: 1260.157 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source |
#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 |
-Non-polymers , 4 types, 147 molecules
#5: Chemical | #6: Chemical | ChemComp-HO / #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 previously determined X-ray crystal structure PDB ID 1RER was rigidly docked into the sub- ...The previously determined X-ray crystal structure PDB ID 1RER was rigidly docked into the sub-tomogram averaged map but no further refinement was performed |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: subtomogram averaging |
-Sample preparation
Component | Name: Sub-tomogram averaged map of post-fusion E1 glycoprotein trimer from Chikungunya virus Type: COMPLEX / Entity ID: #1 / Source: NATURAL |
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Molecular weight | Value: 0.15 MDa / Experimental value: NO |
Source (natural) | Organism: Chikungunya virus strain S27-African prototype |
Buffer solution | pH: 5.1 / Details: Hepes Buffer Saline |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: Sub-volumes picked from liposome membrane surface |
Specimen support | Grid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: EMS Lacey Carbon |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K / Details: blot for 7-8 seconds |
Crystal | Density Matthews: 5.15 Å3/Da / Density % sol: 76.1 % |
Crystal grow | pH: 4 Details: PEG 400, NABR, DETERGENT DDAO, HO3+, VAPOR DIFFUSION, HANGING DROP, PH 4, TEMPERATURE 277.0K PH range: 4 |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company | ||||||||||||||||||||||||
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Microscopy | Model: FEI TITAN KRIOS | ||||||||||||||||||||||||
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM | ||||||||||||||||||||||||
Electron lens | Mode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 53000 X / Nominal defocus max: 5000 nm / Nominal defocus min: 2500 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: COMA FREE | ||||||||||||||||||||||||
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER | ||||||||||||||||||||||||
Image recording | Electron dose: 70 e/Å2 / Avg electron dose per subtomogram: 70 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) | ||||||||||||||||||||||||
Diffraction |
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Diffraction source |
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Detector |
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Radiation |
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Radiation wavelength |
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Reflection | Num. obs: 40912 |
-Processing
Software |
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | |||||||||||||||||||||
Symmetry | Point symmetry: C3 (3 fold cyclic) | |||||||||||||||||||||
3D reconstruction | Resolution: 27.2 Å / Resolution method: FSC 0.5 CUT-OFF / Num. of particles: 590 / Symmetry type: POINT | |||||||||||||||||||||
EM volume selection | Details: low pass filtered map of post-fusion E1--homotrimer crystal structure Num. of tomograms: 40 / Num. of volumes extracted: 591 / Reference model: crystal structure | |||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT / Space: REAL | |||||||||||||||||||||
Atomic model building | PDB-ID: 1RER | |||||||||||||||||||||
Refinement | Method to determine structure: MAD, MIR / Resolution: 27.2→27.2 Å / σ(F): 2 / Stereochemistry target values: ENGH & HUBER
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Refinement step | Cycle: LAST / Resolution: 3.2→20 Å
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LS refinement shell | Highest resolution: 27.2 Å
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