+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-21165 | |||||||||
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Title | De novo designed octahedral nanoparticle O43_dn18 | |||||||||
Map data | O43_dn18 nanoparticle, Negative Stain EM map | |||||||||
Sample |
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Biological species | synthetic construct (others) | |||||||||
Method | single particle reconstruction / negative staining / Resolution: 16.4 Å | |||||||||
Authors | Ward AB / Antanasijevic A | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Elife / Year: 2020 Title: Tailored design of protein nanoparticle scaffolds for multivalent presentation of viral glycoprotein antigens. Authors: George Ueda / Aleksandar Antanasijevic / Jorge A Fallas / William Sheffler / Jeffrey Copps / Daniel Ellis / Geoffrey B Hutchinson / Adam Moyer / Anila Yasmeen / Yaroslav Tsybovsky / Young- ...Authors: George Ueda / Aleksandar Antanasijevic / Jorge A Fallas / William Sheffler / Jeffrey Copps / Daniel Ellis / Geoffrey B Hutchinson / Adam Moyer / Anila Yasmeen / Yaroslav Tsybovsky / Young-Jun Park / Matthew J Bick / Banumathi Sankaran / Rebecca A Gillespie / Philip Jm Brouwer / Peter H Zwart / David Veesler / Masaru Kanekiyo / Barney S Graham / Rogier W Sanders / John P Moore / Per Johan Klasse / Andrew B Ward / Neil P King / David Baker / Abstract: Multivalent presentation of viral glycoproteins can substantially increase the elicitation of antigen-specific antibodies. To enable a new generation of anti-viral vaccines, we designed self- ...Multivalent presentation of viral glycoproteins can substantially increase the elicitation of antigen-specific antibodies. To enable a new generation of anti-viral vaccines, we designed self-assembling protein nanoparticles with geometries tailored to present the ectodomains of influenza, HIV, and RSV viral glycoprotein trimers. We first designed trimers tailored for antigen fusion, featuring N-terminal helices positioned to match the C termini of the viral glycoproteins. Trimers that experimentally adopted their designed configurations were incorporated as components of tetrahedral, octahedral, and icosahedral nanoparticles, which were characterized by cryo-electron microscopy and assessed for their ability to present viral glycoproteins. Electron microscopy and antibody binding experiments demonstrated that the designed nanoparticles presented antigenically intact prefusion HIV-1 Env, influenza hemagglutinin, and RSV F trimers in the predicted geometries. This work demonstrates that antigen-displaying protein nanoparticles can be designed from scratch, and provides a systematic way to investigate the influence of antigen presentation geometry on the immune response to vaccination. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_21165.map.gz | 93.2 MB | EMDB map data format | |
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Header (meta data) | emd-21165-v30.xml emd-21165.xml | 13.7 KB 13.7 KB | Display Display | EMDB header |
Images | emd_21165.png | 109.1 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-21165 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-21165 | HTTPS FTP |
-Validation report
Summary document | emd_21165_validation.pdf.gz | 77.4 KB | Display | EMDB validaton report |
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Full document | emd_21165_full_validation.pdf.gz | 76.5 KB | Display | |
Data in XML | emd_21165_validation.xml.gz | 494 B | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-21165 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-21165 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_21165.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | O43_dn18 nanoparticle, Negative Stain EM map | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.05 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : De novo designed octahedral nanoparticle O43_dn18
Entire | Name: De novo designed octahedral nanoparticle O43_dn18 |
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Components |
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-Supramolecule #1: De novo designed octahedral nanoparticle O43_dn18
Supramolecule | Name: De novo designed octahedral nanoparticle O43_dn18 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all / Details: Negative Stain EM Map |
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Source (natural) | Organism: synthetic construct (others) |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) / Recombinant plasmid: pET28b |
Molecular weight | Theoretical: 880 KDa |
-Macromolecule #1: O43_dn18B
Macromolecule | Name: O43_dn18B / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: synthetic construct (others) |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: MGEEAELAYL LGELAYKLGE YRIAIRAYRI ALKRDPNNAE AWYNLGNAYY KQGDYDEAIE YYQKALELDP NNAEAWYNLG NAYYKQGDYD EAIEYYQKAL ELDPSNLDAA VNLGAATMLT S |
-Macromolecule #2: O43_dn18A
Macromolecule | Name: O43_dn18A / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: synthetic construct (others) |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: MDRCEELARR IAEVVERAKR AGTSEDEIAE SVARVISLVI RALKLSGSSY EVICECVARI VAEIVEALKR SGTSAVEIAK IVARVISEVI RTLKESGSSY EVICECVARI VAEIVEALKR SGTSAAIIAL IVALVISEVI RTLKESGSSF EVILECVIRI VLEIIEALKR ...String: MDRCEELARR IAEVVERAKR AGTSEDEIAE SVARVISLVI RALKLSGSSY EVICECVARI VAEIVEALKR SGTSAVEIAK IVARVISEVI RTLKESGSSY EVICECVARI VAEIVEALKR SGTSAAIIAL IVALVISEVI RTLKESGSSF EVILECVIRI VLEIIEALKR SGTSEQDVML IVMAVLLVVL ATLQLSGSGG WLEHHHHHH |
-Experimental details
-Structure determination
Method | negative staining |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.05 mg/mL | |||||||||
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Buffer | pH: 7.4 Component:
Details: TBS buffer, pH 7.4 | |||||||||
Staining | Type: NEGATIVE / Material: Uranyl Formate Details: Sample diluted to 0.05 mg/mL. 3 uL was applied onto the grid, blotted off, and then stained with 2% uranyl formate for 60 seconds. | |||||||||
Grid | Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: CONTINUOUS | |||||||||
Details | O43_dn18 nanoparticle was purified by SEC, diluted to 0.05mg/ml and loaded onto a grid. |
-Electron microscopy
Microscope | FEI TECNAI SPIRIT |
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Image recording | Film or detector model: TVIPS TEMCAM-F416 (4k x 4k) / Average electron dose: 25.0 e/Å2 |
Electron beam | Acceleration voltage: 120 kV / Electron source: LAB6 |
Electron optics | C2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.5 µm / Nominal defocus min: 1.5 µm |
Experimental equipment | Model: Tecnai Spirit / Image courtesy: FEI Company |