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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-21166 | |||||||||
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Title | De novo designed icosahedral nanoparticle I53_dn5 | |||||||||
![]() | De novo designed icosahedral nanoparticle I53_dn5, Negative stain EM map | |||||||||
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Biological species | synthetic construct (others) | |||||||||
Method | single particle reconstruction / negative staining / Resolution: 18.74 Å | |||||||||
![]() | Ward AB / Antanasijevic A | |||||||||
Funding support | ![]()
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![]() | ![]() 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 |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 11.6 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 14.1 KB 14.1 KB | Display Display | ![]() |
Images | ![]() | 125.6 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 77.4 KB | Display | ![]() |
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Full document | ![]() | 76.5 KB | Display | |
Data in XML | ![]() | 495 B | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | De novo designed icosahedral nanoparticle I53_dn5, Negative stain EM map | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 4.1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
-Entire : De novo designed icosahedral nanoparticle I53_dn5, Negative Stain...
Entire | Name: De novo designed icosahedral nanoparticle I53_dn5, Negative Stain EM Map |
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Components |
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-Supramolecule #1: De novo designed icosahedral nanoparticle I53_dn5, Negative Stain...
Supramolecule | Name: De novo designed icosahedral nanoparticle I53_dn5, Negative Stain EM Map type: complex / ID: 1 / Parent: 0 / Macromolecule list: all Details: Nanoparticles were generated by co-expression of the two components (A and B) in E coli. Assembled particles were purified using a combination of Ni-affinity chromatography and gel filtration chromatography. |
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Source (natural) | Organism: synthetic construct (others) |
Recombinant expression | Organism: ![]() ![]() |
-Macromolecule #1: I53_dn5A
Macromolecule | Name: I53_dn5A / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: synthetic construct (others) |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MGKYDGSKLR IGILHARWNA EIILALVLGA LKRLQEFGVK RENIIIETVP GSFELPYGSK LFVEKQKRLG KPLDAIIPIG VLIKGSTMHF EYICDSTTHQ LMKLNFELGI PVIFGVLTCL TDEQAEARAG LIEGKMHNHG EDWGAAAVEM ATKFN |
-Macromolecule #2: I53_dn5B
Macromolecule | Name: I53_dn5B / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: synthetic construct (others) |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MEEAELAYLL GELAYKLGEY RIAIRAYRIA LKRDPNNAEA WYNLGNAYYK QGRYREAIEY YQKALELDPN NAEAWYNLGN AYYERGEYEE AIEYYRKALR LDPNNADAMQ NLLNAKMREE LEHHHHHH |
-Experimental details
-Structure determination
Method | negative staining |
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![]() | single particle reconstruction |
Aggregation state | particle |
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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 | I53_dn5 nanoparticle was purified by SEC, diluted to 0.05mg/ml and loaded onto a grid. |
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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 |
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Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: RIGID BODY FIT |
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