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- EMDB-47765: Week 26 C3V5, gp41-GH and gp41-base epitope polyclonal antibodies... -

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Basic information

Entry
Database: EMDB / ID: EMD-47765
TitleWeek 26 C3V5, gp41-GH and gp41-base epitope polyclonal antibodies from participant 202 in complex with ConM SOSIP
Map datamain map
Sample
  • Complex: Week 26 C3V5, gp41-GH and gp41-base epitope polyclonal antibodies from participant 202 in complex with ConM SOSIP
KeywordsEMPEM / polyclonal / HIV-1 / ACTHIVE / clinical trial / VIRAL PROTEIN
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / negative staining / Resolution: 30.0 Å
AuthorsLin RN / Torres JL / Tran AS / Ozorowski G / Ward AB
Funding support United States, 1 items
OrganizationGrant numberCountry
Bill & Melinda Gates FoundationINV-002916 United States
CitationJournal: Nat Commun / Year: 2025
Title: HIV-1 envelope trimer vaccine induces sex-associated differences in antibody responses: a phase 1 clinical trial.
Authors: Emma I M M Reiss / Karlijn van der Straten / Laura T M Graus / Marloes Grobben / Kilian E Vlaming / Annelou I P van der Veen / Marinus H Liesdek / Gabriel Ozorowski / Martin Corcoran / ...Authors: Emma I M M Reiss / Karlijn van der Straten / Laura T M Graus / Marloes Grobben / Kilian E Vlaming / Annelou I P van der Veen / Marinus H Liesdek / Gabriel Ozorowski / Martin Corcoran / Hongmei Gao / Kelli M Greene / Nicole L Yates / Sheetal Sawant / Gius Kerster / Judith A Burger / Stella Schonherr / Hannah M Cheeseman / Abbey Evans / Leon R McFarlane / Andy S Tran / Jonathan L Torres / Ryan N Lin / Gyunghee Jo / Monica Tolazzi / Philipp Mundsperger / Dietmar Katinger / Albert Cupo / John P Moore / Rob Hurks / Liffert Vogt / Maarten R Soeters / Neeltje A Kootstra / Gabriella Scarlatti / Georgia D Tomaras / David C Montefiori / Gunilla B Karlsson Hedestam / Andrew B Ward / Michelle Klouwens / Menno D de Jong / Jan M Prins / Mathieu Claireaux / Teunis B H Geijtenbeek / Robin J Shattock / Marit J van Gils / Rogier W Sanders / Godelieve J de Bree /
Abstract: A protective vaccine will be the most powerful instrument to reduce HIV-1 infections worldwide and help bring about a lasting end to the AIDS epidemic. The single centre, randomised, open-label, ...A protective vaccine will be the most powerful instrument to reduce HIV-1 infections worldwide and help bring about a lasting end to the AIDS epidemic. The single centre, randomised, open-label, uncontrolled, phase 1 ACTHIVE-001 clinical trial (NCT03961438) aims to assess the safety and immunogenicity of the ConM SOSIP.v7 native-like trimer protein vaccine, based on an HIV-1 group M consensus sequence, in HIV-negative adults. Twenty-four individuals were enrolled to receive three dosages of ConM SOSIP.v7 protein vaccine in a liposome formulation containing a high dose of the TLR4-agonist MPLA. The primary outcome is vaccine reactogenicity, whereas the main secondary outcome is binding and neutralising antibody responses. Overall, the vaccine is safe and well-tolerated. Furthermore, the vaccine elicits robust strain-specific binding and neutralising antibody responses in nearly all vaccinees. Post-hoc exploratory analyses demonstrate that female-born participants have 22- and 6-fold higher neutralisation titres after the second and third vaccination, respectively. The vaccine adjuvant induces higher levels of IL-6 secretion from in vitro cultured monocytes from female compared to male participants, providing a possible mechanistic explanation for the sex-based differences. Our study highlights the need to take sex-based differences into consideration when assessing HIV-1 vaccine candidates and adjuvants.
History
DepositionNov 7, 2024-
Header (metadata) releaseJan 21, 2026-
Map releaseJan 21, 2026-
UpdateJan 21, 2026-
Current statusJan 21, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_47765.png

Downloads & links

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Map

FileDownload / File: emd_47765.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.)
2.06 Å/pix.
x 192 pix.
= 395.52 Å		2.06 Å/pix.
x 192 pix.
= 395.52 Å		2.06 Å/pix.
x 192 pix.
= 395.52 Å

Surface

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Slices (1/2)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 2.06 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.015
Minimum - Maximum-0.024151266 - 0.095343135
Average (Standard dev.)0.00012211603 (±0.0039252066)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions192192192
Spacing192192192
CellA=B=C: 395.52 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: half map B

Fileemd_47765_half_map_1.map
Annotationhalf map B
Projections & Slices
AxesZYX

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Histogram

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Half map: half map A

Fileemd_47765_half_map_2.map
Annotationhalf map A
Projections & Slices
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Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Week 26 C3V5, gp41-GH and gp41-base epitope polyclonal antibodies...

EntireName: Week 26 C3V5, gp41-GH and gp41-base epitope polyclonal antibodies from participant 202 in complex with ConM SOSIP
Components
  • Complex: Week 26 C3V5, gp41-GH and gp41-base epitope polyclonal antibodies from participant 202 in complex with ConM SOSIP

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Supramolecule #1: Week 26 C3V5, gp41-GH and gp41-base epitope polyclonal antibodies...

SupramoleculeName: Week 26 C3V5, gp41-GH and gp41-base epitope polyclonal antibodies from participant 202 in complex with ConM SOSIP
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Homo sapiens (human)

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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
Component:
ConcentrationNameFormula
50.0 mMTris
150.0 mMSodium chlorideNaCl
StainingType: NEGATIVE / Material: uranyl formate / Details: 2% UF
GridModel: Homemade / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE

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Electron microscopy

MicroscopeFEI TECNAI SPIRIT
Image recordingFilm or detector model: TVIPS TEMCAM-F416 (4k x 4k) / Average electron dose: 25.0 e/Å2
Electron beamAcceleration voltage: 120 kV / Electron source: LAB6
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.5 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Tecnai Spirit / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6v0r


Details: PDB converted to map and low pass filtered to 20 A using UCSF Chimera molmap
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 30.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 3000
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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