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Yorodumi- EMDB-27248: Sub-tomogram averaged map of full-length post-fusion CHIKV E1 gly... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-27248 | |||||||||
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Title | Sub-tomogram averaged map of full-length post-fusion CHIKV E1 glycoprotein trimer | |||||||||
Map data | Sub-tomogram averaged map of membrane attached full-length post-fusion CHIKV E1 glycoprotein trimer | |||||||||
Sample |
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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 / viral translational frameshifting / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane ...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 / viral translational frameshifting / 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 / structural molecule activity / virion membrane / proteolysis / RNA binding / membrane Similarity search - Function | |||||||||
Biological species | Chikungunya virus strain S27-African prototype | |||||||||
Method | subtomogram averaging / cryo EM / Resolution: 27.2 Å | |||||||||
Authors | Mangala Prasad V / Lee KK | |||||||||
Funding support | United States, 2 items
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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
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_27248.map.gz | 232.3 KB | EMDB map data format | |
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Header (meta data) | emd-27248-v30.xml emd-27248.xml | 18.1 KB 18.1 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_27248_fsc.xml | 4.4 KB | Display | FSC data file |
Images | emd_27248.png | 106.7 KB | ||
Others | emd_27248_half_map_1.map.gz emd_27248_half_map_2.map.gz | 232.1 KB 232 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-27248 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-27248 | HTTPS FTP |
-Validation report
Summary document | emd_27248_validation.pdf.gz | 602 KB | Display | EMDB validaton report |
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Full document | emd_27248_full_validation.pdf.gz | 601.6 KB | Display | |
Data in XML | emd_27248_validation.xml.gz | 8.1 KB | Display | |
Data in CIF | emd_27248_validation.cif.gz | 10.1 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-27248 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-27248 | HTTPS FTP |
-Related structure data
Related structure data | 8d87MC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_27248.map.gz / Format: CCP4 / Size: 251 KB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | Sub-tomogram averaged map of membrane attached full-length post-fusion CHIKV E1 glycoprotein trimer | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 6.612 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: Odd-half map
File | emd_27248_half_map_1.map | ||||||||||||
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Annotation | Odd-half map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Even half map
File | emd_27248_half_map_2.map | ||||||||||||
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Annotation | Even half map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Sub-tomogram averaged map of post-fusion E1 glycoprotein trimer f...
Entire | Name: Sub-tomogram averaged map of post-fusion E1 glycoprotein trimer from Chikungunya virus |
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Components |
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-Supramolecule #1: Sub-tomogram averaged map of post-fusion E1 glycoprotein trimer f...
Supramolecule | Name: Sub-tomogram averaged map of post-fusion E1 glycoprotein trimer from Chikungunya virus type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Chikungunya virus strain S27-African prototype |
Molecular weight | Theoretical: 150 KDa |
-Macromolecule #1: Spike glycoprotein E1
Macromolecule | Name: Spike glycoprotein E1 / type: protein_or_peptide / ID: 1 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 Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Chikungunya virus strain S27-African prototype |
Molecular weight | Theoretical: 42.690125 KDa |
Sequence | String: YEHSTVMPNV VGFPYKAHIE RPGYSPLTLQ MQVVETSLEP TLNLEYITCE YKTVVPSPYV KCCGASECST KEKPDYQCKV YTGVYPFMW GGAYCFCDSE NTQLSEAYVD RSDVCRHDHA SAYKAHTASL KAKVRVMYGN VNQTVDVYVN GDHAVTIGGT Q FIFGPLSS ...String: YEHSTVMPNV VGFPYKAHIE RPGYSPLTLQ MQVVETSLEP TLNLEYITCE YKTVVPSPYV KCCGASECST KEKPDYQCKV YTGVYPFMW GGAYCFCDSE NTQLSEAYVD RSDVCRHDHA SAYKAHTASL KAKVRVMYGN VNQTVDVYVN GDHAVTIGGT Q FIFGPLSS AWTPFDNKIV VYKDEVFNQD FPPYGSGQPG RFGDIQSRTV ESNDLYANTA LKLARPSPGM VHVPYTQTPS GF KYWLKEK GTALNTKAPF GCQIKTNPVR AMNCAVGNIP VSMNLPDSAF TRIVEAPTII DLTCTVATCT HSSDFGGVLT LTY KTNKNG DCSVHSHSNV ATLQEATAKV KTAGKVTLHF STASASPSFV VSLCSARATC SASCEPPKDH IVPYA |
-Macromolecule #5: BROMIDE ION
Macromolecule | Name: BROMIDE ION / type: ligand / ID: 5 / Number of copies: 3 / Formula: BR |
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Molecular weight | Theoretical: 79.904 Da |
Chemical component information | ChemComp-BR: |
-Macromolecule #6: HOLMIUM ATOM
Macromolecule | Name: HOLMIUM ATOM / type: ligand / ID: 6 / Number of copies: 4 / Formula: HO |
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Molecular weight | Theoretical: 164.93 Da |
Chemical component information | ChemComp-HO: |
-Macromolecule #7: PHOSPHATE ION
Macromolecule | Name: PHOSPHATE ION / type: ligand / ID: 7 / Number of copies: 1 / Formula: PO4 |
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Molecular weight | Theoretical: 94.971 Da |
Chemical component information | ChemComp-PO4: |
-Macromolecule #8: water
Macromolecule | Name: water / type: ligand / ID: 8 / Number of copies: 139 / Formula: HOH |
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Molecular weight | Theoretical: 18.015 Da |
Chemical component information | ChemComp-HOH: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | subtomogram averaging |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 5.1 / Details: Hepes Buffer Saline |
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Grid | Model: EMS Lacey Carbon / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: LACEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV / Details: blot for 7-8 seconds. |
Details | Sub-volumes picked from liposome membrane surface |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 70.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 5.0 µm / Nominal defocus min: 2.5 µm / Nominal magnification: 53000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |