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- EMDB-43668: Triple tandem trimer immunogens for HIV-1 and influenza nucleic a... -

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Basic information

Entry
Database: EMDB / ID: EMD-43668
TitleTriple tandem trimer immunogens for HIV-1 and influenza nucleic acid-based vaccines (H5/1 GCN4)
Map data
Sample
  • Complex: Chimeric hemagglutinin in complex with CR9114 Fab.
KeywordsHemagglutinin / CR9114 Fab / VIRUS
Biological speciesInfluenza A virus
Methodsingle particle reconstruction / negative staining / Resolution: 19.52 Å
AuthorsFerguson JA / Leon AN / Ward AB
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI110657 United States
CitationJournal: NPJ Vaccines / Year: 2024
Title: Triple tandem trimer immunogens for HIV-1 and influenza nucleic acid-based vaccines.
Authors: Iván Del Moral-Sánchez / Edmund G Wee / Yuejiao Xian / Wen-Hsin Lee / Joel D Allen / Alba Torrents de la Peña / Rebeca Fróes Rocha / James Ferguson / André N León / Sylvie Koekkoek / ...Authors: Iván Del Moral-Sánchez / Edmund G Wee / Yuejiao Xian / Wen-Hsin Lee / Joel D Allen / Alba Torrents de la Peña / Rebeca Fróes Rocha / James Ferguson / André N León / Sylvie Koekkoek / Edith E Schermer / Judith A Burger / Sanjeev Kumar / Robby Zwolsman / Mitch Brinkkemper / Aafke Aartse / Dirk Eggink / Julianna Han / Meng Yuan / Max Crispin / Gabriel Ozorowski / Andrew B Ward / Ian A Wilson / Tomáš Hanke / Kwinten Sliepen / Rogier W Sanders /
Abstract: Recombinant native-like HIV-1 envelope glycoprotein (Env) trimers are used in candidate vaccines aimed at inducing broadly neutralizing antibodies. While state-of-the-art SOSIP or single-chain Env ...Recombinant native-like HIV-1 envelope glycoprotein (Env) trimers are used in candidate vaccines aimed at inducing broadly neutralizing antibodies. While state-of-the-art SOSIP or single-chain Env designs can be expressed as native-like trimers, undesired monomers, dimers and malformed trimers that elicit non-neutralizing antibodies are also formed, implying that these designs could benefit from further modifications for gene-based vaccination approaches. Here, we describe the triple tandem trimer (TTT) design, in which three Env protomers are genetically linked in a single open reading frame and express as native-like trimers. Viral vectored Env TTT induced similar neutralization titers but with a higher proportion of trimer-specific responses. The TTT design was also applied to generate influenza hemagglutinin (HA) trimers without the need for trimerization domains. Additionally, we used TTT to generate well-folded chimeric Env and HA trimers that harbor protomers from three different strains. In summary, the TTT design is a useful platform for the design of HIV-1 Env and influenza HA immunogens for a multitude of vaccination strategies.
History
DepositionFeb 9, 2024-
Header (metadata) releaseApr 17, 2024-
Map releaseApr 17, 2024-
UpdateApr 17, 2024-
Current statusApr 17, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_43668.png

Downloads & links

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Map

FileDownload / File: emd_43668.map.gz / Format: CCP4 / Size: 22.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
2.06 Å/pix.
x 180 pix.
= 370.8 Å		2.06 Å/pix.
x 180 pix.
= 370.8 Å		2.06 Å/pix.
x 180 pix.
= 370.8 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 2.06 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0209
Minimum - Maximum-0.062428463 - 0.09046848
Average (Standard dev.)0.000063885185 (±0.005432799)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions180180180
Spacing180180180
CellA=B=C: 370.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_43668_half_map_1.map
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AxesZYX

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Half map: #2

Fileemd_43668_half_map_2.map
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Sample components

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Entire : Chimeric hemagglutinin in complex with CR9114 Fab.

EntireName: Chimeric hemagglutinin in complex with CR9114 Fab.
Components
  • Complex: Chimeric hemagglutinin in complex with CR9114 Fab.

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Supramolecule #1: Chimeric hemagglutinin in complex with CR9114 Fab.

SupramoleculeName: Chimeric hemagglutinin in complex with CR9114 Fab. / type: complex / ID: 1 / Parent: 0 / Details: (H2/1 GCN4)
Source (natural)Organism: Influenza A virus

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Experimental details

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Structure determination

Methodnegative staining
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.02 mg/mL
BufferpH: 7.4 / Details: Tris-Buffered Saline
StainingType: NEGATIVE / Material: Uranyl formate
GridModel: Homemade / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: CONTINUOUS

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Electron microscopy

MicroscopeFEI TECNAI SPIRIT
Electron beamAcceleration voltage: 120 kV / Electron source: LAB6
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 1.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 52000
Sample stageCooling holder cryogen: NITROGEN
Image recordingFilm or detector model: FEI EAGLE (4k x 4k) / Average electron dose: 25.0 e/Å2
Experimental equipment
Model: Tecnai Spirit / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER / Details: PDB2MRC PDBID 4m4y Low pass filtered to 20A
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final reconstructionResolution.type: BY AUTHOR / Resolution: 19.52 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 9523

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