+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-21167 | |||||||||
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Title | BG505-SOSIP-T33_dn2A nanoparticle fusion component | |||||||||
Map data | Negative Stain EM map of BG505-SOSIP-T33_dn2A fusion component | |||||||||
Sample |
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Biological species | synthetic construct (others) | |||||||||
Method | single particle reconstruction / negative staining / Resolution: 15.62 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_21167.map.gz | 11.8 MB | EMDB map data format | |
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Header (meta data) | emd-21167-v30.xml emd-21167.xml | 13.6 KB 13.6 KB | Display Display | EMDB header |
Images | emd_21167.png | 42.7 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-21167 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-21167 | HTTPS FTP |
-Validation report
Summary document | emd_21167_validation.pdf.gz | 77.7 KB | Display | EMDB validaton report |
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Full document | emd_21167_full_validation.pdf.gz | 76.8 KB | Display | |
Data in XML | emd_21167_validation.xml.gz | 495 B | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-21167 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-21167 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_21167.map.gz / Format: CCP4 / Size: 15.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Negative Stain EM map of BG505-SOSIP-T33_dn2A fusion component | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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 : BG505-SOSIP-T33_dn2A Nanoparticle Fusion Construct
Entire | Name: BG505-SOSIP-T33_dn2A Nanoparticle Fusion Construct |
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Components |
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-Supramolecule #1: BG505-SOSIP-T33_dn2A Nanoparticle Fusion Construct
Supramolecule | Name: BG505-SOSIP-T33_dn2A Nanoparticle Fusion Construct / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all Details: Nanoparticle Fusion Construct. Antigen-presenting component of the T33_dn2 nanoparticle. |
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Source (natural) | Organism: synthetic construct (others) |
Recombinant expression | Organism: Homo sapiens (human) / Recombinant strain: HEK293F / Recombinant plasmid: pPPI4 |
Molecular weight | Theoretical: 259 KDa |
-Macromolecule #1: BG505-SOSIP-T33_dn2A fusion construct
Macromolecule | Name: BG505-SOSIP-T33_dn2A fusion construct / type: protein_or_peptide / ID: 1 / Enantiomer: DEXTRO |
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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 |
-Experimental details
-Structure determination
Method | negative staining |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.02 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 0.02 mg/mL. 3 uL was applied onto the grid, blotted off, and then stained with 2% uranyl formate for 60 seconds. | |||||||||
Grid | Model: Homemade / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE | |||||||||
Details | Sample purified by SEC, mono-disperse |
-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 |