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- EMDB-3292: Sub-tomogram averaging of Lassa virus glycoprotein spike from vir... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-3292 | |||||||||
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Title | Sub-tomogram averaging of Lassa virus glycoprotein spike from virus-like particles at pH 5 | |||||||||
![]() | Sub-tomogram average of the glycoprotein spike trimer | |||||||||
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![]() | lassa virus / membrane protein / glycoprotein / receptor binding / membrane fusion | |||||||||
Function / homology | ![]() host cell Golgi membrane / receptor-mediated endocytosis of virus by host cell / host cell endoplasmic reticulum membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / membrane / metal ion binding Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | subtomogram averaging / cryo EM / Resolution: 16.4 Å | |||||||||
![]() | Li S / Zhaoyang S / Pryce R / Parsy M-L / Fehling SK / Schlie K / Siebert CA / Garten W / Bowden TA / Strecker T / Huiskonen JT | |||||||||
![]() | ![]() Title: Acidic pH-Induced Conformations and LAMP1 Binding of the Lassa Virus Glycoprotein Spike. Authors: Sai Li / Zhaoyang Sun / Rhys Pryce / Marie-Laure Parsy / Sarah K Fehling / Katrin Schlie / C Alistair Siebert / Wolfgang Garten / Thomas A Bowden / Thomas Strecker / Juha T Huiskonen / ![]() ![]() Abstract: Lassa virus is an enveloped, bi-segmented RNA virus and the most prevalent and fatal of all Old World arenaviruses. Virus entry into the host cell is mediated by a tripartite surface spike complex, ...Lassa virus is an enveloped, bi-segmented RNA virus and the most prevalent and fatal of all Old World arenaviruses. Virus entry into the host cell is mediated by a tripartite surface spike complex, which is composed of two viral glycoprotein subunits, GP1 and GP2, and the stable signal peptide. Of these, GP1 binds to cellular receptors and GP2 catalyzes fusion between the viral envelope and the host cell membrane during endocytosis. The molecular structure of the spike and conformational rearrangements induced by low pH, prior to fusion, remain poorly understood. Here, we analyzed the three-dimensional ultrastructure of Lassa virus using electron cryotomography. Sub-tomogram averaging yielded a structure of the glycoprotein spike at 14-Å resolution. The spikes are trimeric, cover the virion envelope, and connect to the underlying matrix. Structural changes to the spike, following acidification, support a viral entry mechanism dependent on binding to the lysosome-resident receptor LAMP1 and further dissociation of the membrane-distal GP1 subunits. | |||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 7.5 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 11.9 KB 11.9 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 4.8 KB | Display | ![]() |
Images | ![]() | 1 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5ft2MC ![]() 3290C ![]() 3291C ![]() 3293C ![]() 3294C M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Sub-tomogram average of the glycoprotein spike trimer | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.7 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
-Entire : Purified Lassa virus VLPs at pH 5
Entire | Name: Purified Lassa virus VLPs at pH 5 |
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Components |
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-Supramolecule #1000: Purified Lassa virus VLPs at pH 5
Supramolecule | Name: Purified Lassa virus VLPs at pH 5 / type: sample / ID: 1000 / Details: Unfixed virus-like particles / Number unique components: 1 |
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-Supramolecule #1: Lassa virus
Supramolecule | Name: Lassa virus / type: virus / ID: 1 / Name.synonym: Lassa mammarenavirus / NCBI-ID: 11620 / Sci species name: Lassa virus / Sci species strain: Josiah / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No / Syn species name: Lassa mammarenavirus |
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Host (natural) | Organism: ![]() |
Host system | Organism: ![]() ![]() |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | subtomogram averaging |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 5.2 Details: 50 mM buffer of succinic acid, dihydrogen phosphate and glycine (2:7:7) |
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Grid | Details: Grids (Cflat CF-2/1-2C-T) were glow-discharged for 15 s. 6-nm gold particles were added. |
Vitrification | Cryogen name: ETHANE-PROPANE MIXTURE / Chamber humidity: 80 % / Chamber temperature: 120 K / Instrument: GATAN CRYOPLUNGE 3 / Method: Blot for 3 seconds before plunging. |
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Electron microscopy
Microscope | FEI POLARA 300 |
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Temperature | Min: 80 K / Max: 120 K |
Alignment procedure | Legacy - Astigmatism: Objective lens astigmatism was corrected at 160,000 times magnification. |
Specialist optics | Energy filter - Name: GIF QUANTUM LS / Energy filter - Lower energy threshold: 0.0 eV / Energy filter - Upper energy threshold: 20.0 eV |
Details | Super-resolution counting mode |
Date | Sep 25, 2014 |
Image recording | Category: CCD / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Digitization - Sampling interval: 5 µm / Number real images: 16 / Average electron dose: 60 e/Å2 Details: Each image is a tilt series of 19 movies, acquired at 5 degree intervals. Each movie consists of 8 frames. |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Calibrated magnification: 37037 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: 6.7 µm / Nominal defocus min: 2.8 µm / Nominal magnification: 160000 |
Sample stage | Specimen holder: Liquid nitrogen cooled / Specimen holder model: OTHER / Tilt series - Axis1 - Min angle: -45 ° / Tilt series - Axis1 - Max angle: 45 ° |
Experimental equipment | ![]() Model: Tecnai Polara / Image courtesy: FEI Company |
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Image processing
-Atomic model buiding 1
Initial model | PDB ID: Chain - Chain ID: B |
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Software | Name: Chimera, Segger |
Details | The GP1 subunit was fitted to different density segments of the spike. 1000 evenly rotated fits were considered. |
Refinement | Space: REAL / Protocol: RIGID BODY FIT / Target criteria: Cross-correlation |
Output model | ![]() PDB-5ft2: |