+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-21174 | |||||||||
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Title | De novo designed icosahedral nanoparticle I53_dn5 | |||||||||
Map data | I53_dn5 Nanoparticle Map | |||||||||
Sample |
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Keywords | De novo / Nanoparticle / DE NOVO PROTEIN | |||||||||
Biological species | synthetic construct (others) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 5.35 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_21174.map.gz | 224.9 MB | EMDB map data format | |
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Header (meta data) | emd-21174-v30.xml emd-21174.xml | 20.1 KB 20.1 KB | Display Display | EMDB header |
Images | emd_21174.png | 217.8 KB | ||
Masks | emd_21174_msk_1.map | 244.1 MB | Mask map | |
Filedesc metadata | emd-21174.cif.gz | 6.2 KB | ||
Others | emd_21174_half_map_1.map.gz emd_21174_half_map_2.map.gz | 193.1 MB 193 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-21174 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-21174 | HTTPS FTP |
-Validation report
Summary document | emd_21174_validation.pdf.gz | 725.1 KB | Display | EMDB validaton report |
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Full document | emd_21174_full_validation.pdf.gz | 724.6 KB | Display | |
Data in XML | emd_21174_validation.xml.gz | 15.8 KB | Display | |
Data in CIF | emd_21174_validation.cif.gz | 18.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-21174 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-21174 | HTTPS FTP |
-Related structure data
Related structure data | 6vfjMC 6v8eC 6vehC 6vfhC 6vfiC 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_21174.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | I53_dn5 Nanoparticle 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_21174_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: I53 dn5 Nanoparticle Half-Map 1
File | emd_21174_half_map_1.map | ||||||||||||
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Annotation | I53_dn5 Nanoparticle Half-Map 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: I53 dn5 Nanoparticle Half-Map 2
File | emd_21174_half_map_2.map | ||||||||||||
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Annotation | I53_dn5 Nanoparticle Half-Map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : De novo designed nanoparticle of icosahedral symmetry I53_dn5_NP
Entire | Name: De novo designed nanoparticle of icosahedral symmetry I53_dn5_NP |
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Components |
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-Supramolecule #1: De novo designed nanoparticle of icosahedral symmetry I53_dn5_NP
Supramolecule | Name: De novo designed nanoparticle of icosahedral symmetry I53_dn5_NP type: complex / ID: 1 / Parent: 0 / Macromolecule list: all Details: Self-assembling nanoparticle of icosahedral symmetry |
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Source (natural) | Organism: synthetic construct (others) |
Molecular weight | Theoretical: 1.96 MDa |
-Macromolecule #1: I53_dn5B
Macromolecule | Name: I53_dn5B / 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: 15.356009 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: MEEAELAYLL GELAYKLGEY RIAIRAYRIA LKRDPNNAEA WYNLGNAYYK QGRYREAIEY YQKALELDPN NAEAWYNLGN AYYERGEYE EAIEYYRKAL RLDPNNADAM QNLLNAKMRE ELEHHHHHH |
-Macromolecule #2: I53_dn5A
Macromolecule | Name: I53_dn5A / 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: 17.215148 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: MGKYDGSKLR IGILHARWNA EIILALVLGA LKRLQEFGVK RENIIIETVP GSFELPYGSK LFVEKQKRLG KPLDAIIPIG VLIKGSTMH FEYICDSTTH QLMKLNFELG IPVIFGVLTC LTDEQAEARA GLIEGKMHNH GEDWGAAAVE MATKFN |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 1.9 mg/mL | |||||||||
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Buffer | pH: 7.4 Component:
Details: Fresh 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 / 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 | Nanoparticle was generated by co-expression of two components (A and B) in E coli. Assembled particles purified using a combination of Ni-affinity chromatography 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: 1548 / 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 | Icosahedral nanoparticle I53_dn5 model was docked into a reconstructed map using UCSF Chimera and Rosetta relaxed refinement was applied to relax the model into the map. |
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Refinement | Space: REAL / Protocol: OTHER |
Output model | PDB-6vfj: |