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Yorodumi- EMDB-25108: I53-50 nanoparticle core reconstructed from GPC-I53-50NP by focus... -
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-Basic information
Entry | Database: EMDB / ID: EMD-25108 | |||||||||
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Title | I53-50 nanoparticle core reconstructed from GPC-I53-50NP by focused refinement | |||||||||
Map data | I53-50 nanoparticle map reconstructed from GPC-I53-50 nanoparticle by focused refinement - Main map | |||||||||
Sample |
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Biological species | synthetic construct (others) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.67 Å | |||||||||
Authors | Antanasijevic A / Brouwer PJM / Ward AB | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Cell Host Microbe / Year: 2022 Title: Lassa virus glycoprotein nanoparticles elicit neutralizing antibody responses and protection. Authors: Philip J M Brouwer / Aleksandar Antanasijevic / Adam J Ronk / Helena Müller-Kräuter / Yasunori Watanabe / Mathieu Claireaux / Hailee R Perrett / Tom P L Bijl / Marloes Grobben / Jeffrey C ...Authors: Philip J M Brouwer / Aleksandar Antanasijevic / Adam J Ronk / Helena Müller-Kräuter / Yasunori Watanabe / Mathieu Claireaux / Hailee R Perrett / Tom P L Bijl / Marloes Grobben / Jeffrey C Umotoy / Angela I Schriek / Judith A Burger / Khadija Tejjani / Nicole M Lloyd / Thijs H Steijaert / Marlies M van Haaren / Kwinten Sliepen / Steven W de Taeye / Marit J van Gils / Max Crispin / Thomas Strecker / Alexander Bukreyev / Andrew B Ward / Rogier W Sanders / Abstract: The Lassa virus is endemic in parts of West Africa, and it causes hemorrhagic fever with high mortality. The development of a recombinant protein vaccine has been hampered by the instability of ...The Lassa virus is endemic in parts of West Africa, and it causes hemorrhagic fever with high mortality. The development of a recombinant protein vaccine has been hampered by the instability of soluble Lassa virus glycoprotein complex (GPC) trimers, which disassemble into monomeric subunits after expression. Here, we use two-component protein nanoparticles consisting of trimeric and pentameric subunits to stabilize GPC in a trimeric conformation. These GPC nanoparticles present twenty prefusion GPC trimers on the surface of an icosahedral particle. Cryo-EM studies of GPC nanoparticles demonstrated a well-ordered structure and yielded a high-resolution structure of an unliganded GPC. These nanoparticles induced potent humoral immune responses in rabbits and protective immunity against the lethal Lassa virus challenge in guinea pigs. Additionally, we isolated a neutralizing antibody that mapped to the putative receptor-binding site, revealing a previously undefined site of vulnerability. Collectively, these findings offer potential approaches to vaccine and therapeutic design for the Lassa virus. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_25108.map.gz | 501.8 MB | EMDB map data format | |
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Header (meta data) | emd-25108-v30.xml emd-25108.xml | 21.5 KB 21.5 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_25108_fsc.xml | 18.4 KB | Display | FSC data file |
Images | emd_25108.png | 194.8 KB | ||
Masks | emd_25108_msk_1.map | 536.4 MB | Mask map | |
Others | emd_25108_half_map_1.map.gz emd_25108_half_map_2.map.gz | 428.3 MB 428.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-25108 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-25108 | HTTPS FTP |
-Related structure data
Related structure data | 7sgeMC 7sgdC 7sgfC C: citing same article (ref.) M: atomic model generated by this map |
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-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_25108.map.gz / Format: CCP4 / Size: 536.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | I53-50 nanoparticle map reconstructed from GPC-I53-50 nanoparticle by focused refinement - Main map | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.03 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_25108_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: I53-50 nanoparticle map reconstructed from GPC-I53-50 nanoparticle by...
File | emd_25108_half_map_1.map | ||||||||||||
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Annotation | I53-50 nanoparticle map reconstructed from GPC-I53-50 nanoparticle by focused refinement - Half Map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: I53-50 nanoparticle map reconstructed from GPC-I53-50 nanoparticle by...
File | emd_25108_half_map_2.map | ||||||||||||
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Annotation | I53-50 nanoparticle map reconstructed from GPC-I53-50 nanoparticle by focused refinement - Half Map 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : I53-50 nanoparticle core recovered from GPC-I53-50 nanoparticle
Entire | Name: I53-50 nanoparticle core recovered from GPC-I53-50 nanoparticle |
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Components |
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-Supramolecule #1: I53-50 nanoparticle core recovered from GPC-I53-50 nanoparticle
Supramolecule | Name: I53-50 nanoparticle core recovered from GPC-I53-50 nanoparticle type: complex / ID: 1 / Parent: 0 / Macromolecule list: all Details: Nanoparticle consists of 60 monomeric I53-50A and 60 monomeric I53-50B building blocks. Nanoparticle was assembled by combining equimolar amounts of GPC-I53-50A and I53-50B. |
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Source (natural) | Organism: synthetic construct (others) |
-Macromolecule #1: Josiah GPCysR4-I53-50A - nanoparticle component
Macromolecule | Name: Josiah GPCysR4-I53-50A - nanoparticle component / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: synthetic construct (others) |
Molecular weight | Theoretical: 73.84557 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MGQIVTFFQE VPHVIEEVMN IVLIALSVLA VLKGLYNFAT CGLVGLVTFL LLCGRSCTTS LYKGVYELQT LELNMETLNM TMPLSCTKN NSHHYIMVGN ETGLELTLTN TSIINHKFCN LSDAHKKNLY DHALMSIIST FHLSIPNFNQ YEAMSCDFNG G KISVQYNL ...String: MGQIVTFFQE VPHVIEEVMN IVLIALSVLA VLKGLYNFAT CGLVGLVTFL LLCGRSCTTS LYKGVYELQT LELNMETLNM TMPLSCTKN NSHHYIMVGN ETGLELTLTN TSIINHKFCN LSDAHKKNLY DHALMSIIST FHLSIPNFNQ YEAMSCDFNG G KISVQYNL SHSYAGDAAN HCGTVANGVL QTFMRMAWGG SYIALDSGCG NWDCIMTSYQ YLIIQNTTWE DHCQFSRPSP IG YLGLLSQ RTRDIYISRR RRGTFTWTLS DSEGKDTPGG YCLTRWMLIE AELKCFGNTA VAKCNEKHDE EFCDMLRLFD FNK QAIQRL KAPAQMSIQL INKAVNALIN DQLIMKNHLR DIMCIPYCNY SKYWYLNHTT TGRTSLPKCW LVSNGSYLNE THFS DDIEQ QADNMITEML QKEYMERQGG SGGSGGSGGS GGSEKAAKAE EAARKMEELF KKHKIVAVLR ANSVEEAIEK AVAVF AGGV HLIEITFTVP DADTVIKALS VLKEKGAIIG AGTVTSVEQC RKAVESGAEF IVSPHLDEEI SQFCKEKGVF YMPGVM TPT ELVKAMKLGH DILKLFPGEV VGPEFVKAMK GPFPNVKFVP TGGVDLDNVC EWFDAGVLAV GVGDALVEGD PDEVREK AK EFVEKIRGCT EGSLEWSHPQ FEK |
-Macromolecule #2: I53-50B component
Macromolecule | Name: I53-50B component / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: synthetic construct (others) |
Molecular weight | Theoretical: 18.236877 KDa |
Recombinant expression | Organism: Escherichia coli BL21 (bacteria) |
Sequence | String: MNQHSHKDHE TVRIAVVRAR WHAEIVDACV SAFEAAMRDI GGDRFAVDVF DVPGAYEIPL HARTLAETGR YGAVLGTAFV VNGGIYRHE FVASAVINGM MNVQLNTGVP VLSAVLTPHN YDKSKAHTLL FLALFAVKGM EAARACVEIL AAREKIAAGS L EHHHHHH |
-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 Component:
Details: TBS | |||||||||
Grid | Model: Quantifoil R2/1 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 7 sec. / Pretreatment - Atmosphere: OTHER | |||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 283 K / Instrument: FEI VITROBOT MARK IV / Details: Blot time 4s, Wait time 10s, Blot force 0. | |||||||||
Details | I53-50 nanoparticle core recovered from GPC-I53-50 nanoparticle by focused refinement of the core. Nanoparticle was assembled by combining equimolar amounts of GPC-I53-50A and I53-50B. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 1.6 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 29000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 2 / Number real images: 2337 / Average exposure time: 10.5 sec. / Average electron dose: 50.4 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |