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- EMDB-42464: chEnv TTT protein in complex with 43A2 Fab -

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Basic information

Entry
Database: EMDB / ID: EMD-42464
TitlechEnv TTT protein in complex with 43A2 Fab
Map datamain map
Sample
  • Complex: chEnv TTT protein in complex with 43A2 Fab
    • Complex: chEnv TTT protein in complex with 43A2 Fab
KeywordsHIV / Env / chimeric protein / monoclonal antibody / triple tandem trimer / TTT / VIRAL PROTEIN
Biological speciesHuman immunodeficiency virus 1 / Macaca mulatta (Rhesus monkey)
Methodsingle particle reconstruction / negative staining / Resolution: 28.0 Å
AuthorsOzorowski G / Lee W-H / Ward AB
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)P01 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
DepositionOct 23, 2023-
Header (metadata) releaseApr 24, 2024-
Map releaseApr 24, 2024-
UpdateApr 24, 2024-
Current statusApr 24, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_42464.png

Downloads & links

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Map

FileDownload / File: emd_42464.map.gz / Format: CCP4 / Size: 27 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationmain map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.98 Å/pix.
x 192 pix.
= 380.16 Å		1.98 Å/pix.
x 192 pix.
= 380.16 Å		1.98 Å/pix.
x 192 pix.
= 380.16 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.98 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.015
Minimum - Maximum-0.033519402 - 0.07569014
Average (Standard dev.)-0.000095982585 (±0.003963016)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions192192192
Spacing192192192
CellA=B=C: 380.16 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: half map A

Fileemd_42464_half_map_1.map
Annotationhalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map B

Fileemd_42464_half_map_2.map
Annotationhalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : chEnv TTT protein in complex with 43A2 Fab

EntireName: chEnv TTT protein in complex with 43A2 Fab
Components
  • Complex: chEnv TTT protein in complex with 43A2 Fab
    • Complex: chEnv TTT protein in complex with 43A2 Fab

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Supramolecule #1: chEnv TTT protein in complex with 43A2 Fab

SupramoleculeName: chEnv TTT protein in complex with 43A2 Fab / type: complex / ID: 1 / Parent: 0 / Details: chEnv TTT protein
Source (natural)Organism: Human immunodeficiency virus 1

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Supramolecule #2: chEnv TTT protein in complex with 43A2 Fab

SupramoleculeName: chEnv TTT protein in complex with 43A2 Fab / type: complex / ID: 2 / Parent: 1 / Details: 43A2 Fab
Source (natural)Organism: Macaca mulatta (Rhesus monkey)

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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
StainingType: NEGATIVE / Material: uranyl formate / Details: 2% uranyl formate
GridModel: Homemade / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Pretreatment - Type: GLOW DISCHARGE

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Electron microscopy

MicroscopeTFS TALOS
Image recordingFilm or detector model: FEI CETA (4k x 4k) / Average electron dose: 25.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.5 µm / Nominal defocus min: 1.0 µm

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6v0r


Details: map simulated from coordinates and low pass filtered to 20 Angstrom
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 28.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 16555
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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