+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-21173 | |||||||||
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Title | De novo designed octahedral nanoparticle O43_dn18 | |||||||||
Map data | De novo designed octahedral nanoparticle O43_dn18, Cryo EM map | |||||||||
Sample |
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Biological species | synthetic construct (others) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.54 Å | |||||||||
Authors | Antanasijevic A / Ward AB | |||||||||
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_21173.map.gz | 95.4 MB | EMDB map data format | |
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Header (meta data) | emd-21173-v30.xml emd-21173.xml | 20.8 KB 20.8 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_21173_fsc.xml | 10.7 KB | Display | FSC data file |
Images | emd_21173.png | 224.4 KB | ||
Masks | emd_21173_msk_1.map | 103 MB | Mask map | |
Others | emd_21173_half_map_1.map.gz emd_21173_half_map_2.map.gz | 76.2 MB 76.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-21173 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-21173 | HTTPS FTP |
-Validation report
Summary document | emd_21173_validation.pdf.gz | 753 KB | Display | EMDB validaton report |
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Full document | emd_21173_full_validation.pdf.gz | 752.6 KB | Display | |
Data in XML | emd_21173_validation.xml.gz | 17.8 KB | Display | |
Data in CIF | emd_21173_validation.cif.gz | 23.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-21173 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-21173 | HTTPS FTP |
-Related structure data
Related structure data | 6vfiMC 6v8eC 6vehC 6vfhC 6vfjC M: atomic model generated by this map C: citing same article (ref.) |
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Similar 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_21173.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | De novo designed octahedral nanoparticle O43_dn18, Cryo EM map | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.03 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
File | emd_21173_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: De novo designed octahedral nanoparticle O43 dn18, Cryo EM Half-map 1
File | emd_21173_half_map_1.map | ||||||||||||
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Annotation | De novo designed octahedral nanoparticle O43_dn18, Cryo EM Half-map 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: De novo designed octahedral nanoparticle O43 dn18, Cryo EM Half-map 2
File | emd_21173_half_map_2.map | ||||||||||||
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Annotation | De novo designed octahedral nanoparticle O43_dn18, Cryo EM Half-map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : De novo designed nanoparticle of octahedral symmetry O43_dn18_NP
Entire | Name: De novo designed nanoparticle of octahedral symmetry O43_dn18_NP |
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Components |
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-Supramolecule #1: De novo designed nanoparticle of octahedral symmetry O43_dn18_NP
Supramolecule | Name: De novo designed nanoparticle of octahedral symmetry O43_dn18_NP type: complex / ID: 1 / Parent: 0 / Macromolecule list: all Details: Self-assembling nanoparticle of octahedral symmetry |
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Source (natural) | Organism: synthetic construct (others) |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Molecular weight | Theoretical: 810 KDa |
-Macromolecule #1: O43_dn18B
Macromolecule | Name: O43_dn18B / 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: 13.828147 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: MGEEAELAYL LGELAYKLGE YRIAIRAYRI ALKRDPNNAE AWYNLGNAYY KQGDYDEAIE YYQKALELDP NNAEAWYNLG NAYYKQGDY DEAIEYYQKA LELDPSNLDA AVNLGAATML TS |
-Macromolecule #2: O43_dn18A
Macromolecule | Name: O43_dn18A / 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: 22.722627 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: MDRCEELARR IAEVVERAKR AGTSEDEIAE SVARVISLVI RALKLSGSSY EVICECVARI VAEIVEALKR SGTSAVEIAK IVARVISEV IRTLKESGSS YEVICECVAR IVAEIVEALK RSGTSAAIIA LIVALVISEV IRTLKESGSS FEVILECVIR I VLEIIEAL ...String: MDRCEELARR IAEVVERAKR AGTSEDEIAE SVARVISLVI RALKLSGSSY EVICECVARI VAEIVEALKR SGTSAVEIAK IVARVISEV IRTLKESGSS YEVICECVAR IVAEIVEALK RSGTSAAIIA LIVALVISEV IRTLKESGSS FEVILECVIR I VLEIIEAL KRSGTSEQDV MLIVMAVLLV VLATLQLSGS GGWLEHHHHH H |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 3.0 mg/mL | |||||||||
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Buffer | pH: 7.4 Component:
Details: TBS buffer, 0.2um filtered, 0.06mM DDM detergent added immediately before freezing | |||||||||
Grid | Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 11.0 nm / Details: unspecified | |||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 283 K / Instrument: FEI VITROBOT MARK IV Details: 0.06mM DDM detergent (from an 8X stock) added immediately before freezing. | |||||||||
Details | Nanoparticles were generated by co-expression of the two components (A and B) in E coli. Assembled particles are purified by a combination of Ni-affinity and gel filtration chromatography. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Temperature | Min: 70.0 K / Max: 90.0 K |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 1336 / Average electron dose: 50.4 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 29000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Details | Octahedral nanoparticle O43_dn18 model was fit into the map using UCSF Chimera. A combination of Rosetta relaxed refinement and manual refinement in Coot was used to relax the model into the map. |
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Refinement | Space: REAL / Protocol: OTHER |
Output model | PDB-6vfi: |