+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-41302 | |||||||||
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Title | Lassa GPC trimer in complex with Fab GP23 | |||||||||
Map data | sharpened map | |||||||||
Sample |
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Keywords | vaccine / GPC / GP1 / GP2 / VIRAL PROTEIN | |||||||||
Biological species | Lassa virus Josiah / Cavia porcellus (domestic guinea pig) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 5.4 Å | |||||||||
Authors | Gorman J / Kwong PD | |||||||||
Funding support | United States, 2 items
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Citation | Journal: Nat Commun / Year: 2024 Title: Cleavage-intermediate Lassa virus trimer elicits neutralizing responses, identifies neutralizing nanobodies, and reveals an apex-situated site-of-vulnerability. Authors: Jason Gorman / Crystal Sao-Fong Cheung / Zhijian Duan / Li Ou / Maple Wang / Xuejun Chen / Cheng Cheng / Andrea Biju / Yaping Sun / Pengfei Wang / Yongping Yang / Baoshan Zhang / Jeffrey C ...Authors: Jason Gorman / Crystal Sao-Fong Cheung / Zhijian Duan / Li Ou / Maple Wang / Xuejun Chen / Cheng Cheng / Andrea Biju / Yaping Sun / Pengfei Wang / Yongping Yang / Baoshan Zhang / Jeffrey C Boyington / Tatsiana Bylund / Sam Charaf / Steven J Chen / Haijuan Du / Amy R Henry / Tracy Liu / Edward K Sarfo / Chaim A Schramm / Chen-Hsiang Shen / Tyler Stephens / I-Ting Teng / John-Paul Todd / Yaroslav Tsybovsky / Raffaello Verardi / Danyi Wang / Shuishu Wang / Zhantong Wang / Cheng-Yan Zheng / Tongqing Zhou / Daniel C Douek / John R Mascola / David D Ho / Mitchell Ho / Peter D Kwong / Abstract: Lassa virus (LASV) infection is expanding outside its traditionally endemic areas in West Africa, posing a pandemic biothreat. LASV-neutralizing antibodies, moreover, have proven difficult to elicit. ...Lassa virus (LASV) infection is expanding outside its traditionally endemic areas in West Africa, posing a pandemic biothreat. LASV-neutralizing antibodies, moreover, have proven difficult to elicit. To gain insight into LASV neutralization, here we develop a prefusion-stabilized LASV glycoprotein trimer (GPC), pan it against phage libraries comprising single-domain antibodies (nanobodies) from shark and camel, and identify one, D5, which neutralizes LASV. Cryo-EM analyses reveal D5 to recognize a cleavage-dependent site-of-vulnerability at the trimer apex. The recognized site appears specific to GPC intermediates, with protomers lacking full cleavage between GP1 and GP2 subunits. Guinea pig immunizations with the prefusion-stabilized cleavage-intermediate LASV GPC, first as trimer and then as a nanoparticle, induce neutralizing responses, targeting multiple epitopes including that of D5; we identify a neutralizing antibody (GP23) from the immunized guinea pigs. Collectively, our findings define a prefusion-stabilized GPC trimer, reveal an apex-situated site-of-vulnerability, and demonstrate elicitation of LASV-neutralizing responses by a cleavage-intermediate LASV trimer. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_41302.map.gz | 229.6 MB | EMDB map data format | |
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Header (meta data) | emd-41302-v30.xml emd-41302.xml | 18.3 KB 18.3 KB | Display Display | EMDB header |
Images | emd_41302.png | 48.7 KB | ||
Masks | emd_41302_msk_1.map | 244.1 MB | Mask map | |
Filedesc metadata | emd-41302.cif.gz | 4.7 KB | ||
Others | emd_41302_additional_1.map.gz emd_41302_half_map_1.map.gz emd_41302_half_map_2.map.gz | 120.4 MB 226.2 MB 226.2 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-41302 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-41302 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_41302.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | sharpened map | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.083 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_41302_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: unsharpened map
File | emd_41302_additional_1.map | ||||||||||||
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Annotation | unsharpened map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half map A
File | emd_41302_half_map_1.map | ||||||||||||
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Annotation | half map A | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half map B
File | emd_41302_half_map_2.map | ||||||||||||
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Annotation | half map B | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Lassa GPC Trimer in complex with Fab GP23
Entire | Name: Lassa GPC Trimer in complex with Fab GP23 |
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Components |
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-Supramolecule #1: Lassa GPC Trimer in complex with Fab GP23
Supramolecule | Name: Lassa GPC Trimer in complex with Fab GP23 / type: complex / ID: 1 / Parent: 0 |
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-Supramolecule #2: Lassa GPC Trimer
Supramolecule | Name: Lassa GPC Trimer / type: complex / ID: 2 / Parent: 1 |
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Source (natural) | Organism: Lassa virus Josiah |
-Supramolecule #3: Fab GP23
Supramolecule | Name: Fab GP23 / type: complex / ID: 3 / Parent: 1 |
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Source (natural) | Organism: Cavia porcellus (domestic guinea pig) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 2 mg/mL |
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Buffer | pH: 7.4 / Details: PBS |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 293 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.8 µm |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Average exposure time: 2.0 sec. / Average electron dose: 51.37 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: NONE |
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Initial angle assignment | Type: NOT APPLICABLE |
Final 3D classification | Software - Name: cryoSPARC (ver. 3) |
Final angle assignment | Type: NOT APPLICABLE |
Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 5.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3) / Number images used: 164661 |
-Atomic model buiding 1
Refinement | Space: REAL |
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