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Yorodumi- EMDB-21169: De novo designed tetrahedral nanoparticle T33_dn2 presenting BG50... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-21169 | |||||||||
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Title | De novo designed tetrahedral nanoparticle T33_dn2 presenting BG505-SOSIP | |||||||||
Map data | Tetrahedral nanoparticle T33_dn2 presenting BG505-SOSIP, Negative stain EM map | |||||||||
Sample |
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Biological species | synthetic construct (others) | |||||||||
Method | single particle reconstruction / negative staining / Resolution: 34.17 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_21169.map.gz | 9.8 MB | EMDB map data format | |
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Header (meta data) | emd-21169-v30.xml emd-21169.xml | 14.3 KB 14.3 KB | Display Display | EMDB header |
Images | emd_21169.png | 134.9 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-21169 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-21169 | HTTPS FTP |
-Validation report
Summary document | emd_21169_validation.pdf.gz | 77.7 KB | Display | EMDB validaton report |
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Full document | emd_21169_full_validation.pdf.gz | 76.8 KB | Display | |
Data in XML | emd_21169_validation.xml.gz | 495 B | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-21169 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-21169 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_21169.map.gz / Format: CCP4 / Size: 12.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Tetrahedral nanoparticle T33_dn2 presenting BG505-SOSIP, 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
-Sample components
-Entire : Tetrahedral nanoparticle, T33_dn2, presenting BG505-SOSIP
Entire | Name: Tetrahedral nanoparticle, T33_dn2, presenting BG505-SOSIP |
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Components |
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-Supramolecule #1: Tetrahedral nanoparticle, T33_dn2, presenting BG505-SOSIP
Supramolecule | Name: Tetrahedral nanoparticle, T33_dn2, presenting BG505-SOSIP type: complex / ID: 1 / Parent: 0 / Macromolecule list: all / Details: 4 copies of BG505-SOSIP presented |
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Source (natural) | Organism: synthetic construct (others) |
Recombinant expression | Organism: Homo sapiens (human) / Recombinant strain: HEK293F / Recombinant plasmid: pPPI4 |
-Macromolecule #1: BG505-SOSIP-T33_dn2A
Macromolecule | Name: BG505-SOSIP-T33_dn2A / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: synthetic construct (others) |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MKRGLCCVLL LCGAVFVSPS QEIHARFRRG ARAENLWVTV YYGVPVWKDA ETTLFCASDA KAYETKKHNV WATHCCVPTD PNPQEIHLEN VTEEFNMWKN NMVEQMHTDI ISLWDQSLKP CVKLTPLCVT LQCTNVTNNI TDDMRGELKN CSFNMTTELR DKKQKVYSLF ...String: MKRGLCCVLL LCGAVFVSPS QEIHARFRRG ARAENLWVTV YYGVPVWKDA ETTLFCASDA KAYETKKHNV WATHCCVPTD PNPQEIHLEN VTEEFNMWKN NMVEQMHTDI ISLWDQSLKP CVKLTPLCVT LQCTNVTNNI TDDMRGELKN CSFNMTTELR DKKQKVYSLF YRLDVVQINE NQGNRSNNSN KEYRLINCNT SAITQACPKV SFEPIPIHYC APAGFAILKC KDKKFNGTGP CTNVSTVQCT HGIKPVVSTQ LLLNGSLAEE EVIIRSENIT NNAKNILVQL NESVQINCTR PNNNTVKSIR IGPGQWFYYT GDIIGDIRQA HCNVSKATWN ETLGKVVKQL RKHFGNNTII RFANSSGGDL EVTTHSFNCG GEFFYCNTSG LFNSTWISNT SVQGSNSTGS NDSITLPCRI KQIINMWQRI GQAMYAPPIQ GVIRCVSNIT GLILTRDGGS TNSTTETFRP GGGDMRDNWR SELYKYKVVK IEPLGVAPTR CKRRVVGRRR RRRAVGIGAV SLGFLGAAGS TMGAASMTLT VQARNLLSGI VQQQSNLLRA PECQQHLLKD THWGIKQLQA RVLAVEHYLR DQQLLGIWGC SGKLICCTNV PWNSSWSNRN LSEIWDNMTW LQWDKEISNY TQIIYGLLEE SQNQQEKNEQ DLLELDKWAS LWGSMGNLAE KMYKAGNAMY RKGQYTIAII AYTLALLKDP NNAEAWYNLG NAAYKKGEYD EAIEAYQKAL ELDPNNAEAW YNLGNAYYKQ GDYDEAIEYY KKALRLDPRN VDAIENLIEA EEKQGAS |
-Macromolecule #2: T33_dn2B
Macromolecule | Name: T33_dn2B / 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: MEEAELAYLL GELAYKLGEY RIAIRAYRIA LKRDPNNAEA WYNLGNAYYK QGDYREAIRY YLRALKLDPE NAEAWYNLGN ALYKQGKYDL AIIAYQAALE EDPNNAEAKQ NLGNAKQKQG LEHHHHHH |
-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 | BG505-SOSIP-T33_dn2 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 |