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- EMDB-70491: BG505 GT1.1 SOSIP in complex with V1V2V3 epitope polyclonal antib... -

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Entry
Database: EMDB / ID: EMD-70491
TitleBG505 GT1.1 SOSIP in complex with V1V2V3 epitope polyclonal antibodies isolated from a participant in the IAVI C101 clinical trial
Map datamain map
Sample
  • Complex: BG505 GT1.1 SOSIP in complex with V1V2V3 epitope polyclonal antibodies isolated from a participant in the IAVI C101 clinical trial
KeywordsHIV-1 / Env / germline targeting / VRC01 / VIRAL PROTEIN / EMPEM
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / negative staining / Resolution: 30.0 Å
AuthorsOzorowski G / Ward AB
Funding support United States, 1 items
OrganizationGrant numberCountry
Bill & Melinda Gates FoundationINV-002916 United States
CitationJournal: Science / Year: 2025
Title: Precise targeting of HIV broadly neutralizing antibody precursors in humans.
Authors: Tom G Caniels / Madhu Prabhakaran / Gabriel Ozorowski / Kellie J MacPhee / Weiwei Wu / Karlijn van der Straten / Sashank Agrawal / Ronald Derking / Emma I M M Reiss / Katrina Millard / ...Authors: Tom G Caniels / Madhu Prabhakaran / Gabriel Ozorowski / Kellie J MacPhee / Weiwei Wu / Karlijn van der Straten / Sashank Agrawal / Ronald Derking / Emma I M M Reiss / Katrina Millard / Martina Turroja / Aimee Desrosiers / Jeffrey Bethony / Elissa Malkin / Marinus H Liesdek / Annelou van der Veen / Michelle Klouwens / Jonne L Snitselaar / Joey H Bouhuijs / Rhianna Bronson / Jalen Jean-Baptiste / Suprabhath Gajjala / Zahra Rikhtegaran Tehrani / Alison Benner / Mukundhan Ramaswami / Michael O Duff / Yung-Wen Liu / Alicia H Sato / Ju Yeong Kim / Isabel J L Baken / Catarina Mendes Silva / Tom P L Bijl / Jacqueline van Rijswijk / Judith A Burger / Albert Cupo / Anila Yasmeen / Swastik Phulera / Wen-Hsin Lee / Kipchoge N Randall / Shiyu Zhang / Martin M Corcoran / Isabel Regadas / Alex C Sullivan / David M Brown / Jennifer A Bohl / Kelli M Greene / Hongmei Gao / Nicole L Yates / Sheetal Sawant / Jan M Prins / Neeltje A Kootstra / Stephen M Kaminsky / Burc Barin / Farhad Rahaman / Margaret Meller / Vince Philiponis / Dagna S Laufer / Angela Lombardo / Lindsey Mwoga / Solmaz Shotorbani / Drienna Holman / Richard A Koup / Per Johan Klasse / Gunilla B Karlsson Hedestam / Georgia D Tomaras / Marit J van Gils / David C Montefiori / Adrian B McDermott / Ollivier Hyrien / John P Moore / Ian A Wilson / Andrew B Ward / David J Diemert / Godelieve J de Bree / Sarah F Andrews / Marina Caskey / Rogier W Sanders /
Abstract: A protective HIV vaccine will need to induce broadly neutralizing antibodies (bnAbs) in humans, but priming rare bnAb precursor B cells has been challenging. In a double-blinded, placebo-controlled ...A protective HIV vaccine will need to induce broadly neutralizing antibodies (bnAbs) in humans, but priming rare bnAb precursor B cells has been challenging. In a double-blinded, placebo-controlled phase 1 human clinical trial, the recombinant, germline-targeting envelope glycoprotein (Env) trimer BG505 SOSIP.v4.1-GT1.1, adjuvanted with AS01, induced bnAb precursors of the VRC01-class at a high frequency in the majority of vaccine recipients. These bnAb precursors, that target the CD4 receptor binding site, had undergone somatic hypermutation characteristic of the VRC01-class. A subset of isolated VRC01-class monoclonal antibodies neutralized wild-type pseudoviruses and was structurally extremely similar to bnAb VRC01. These results further support germline-targeting approaches for human HIV vaccine design and demonstrate atomic-level manipulation of B cell responses with rational vaccine design.
History
DepositionMay 4, 2025-
Header (metadata) releaseMay 21, 2025-
Map releaseMay 21, 2025-
UpdateMay 28, 2025-
Current statusMay 28, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_70491.png

Downloads & links

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Map

FileDownload / File: emd_70491.map.gz / Format: CCP4 / Size: 3.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationmain map
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
3.35 Å/pix.
x 96 pix.
= 321.984 Å		3.35 Å/pix.
x 96 pix.
= 321.984 Å		3.35 Å/pix.
x 96 pix.
= 321.984 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 3.354 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.02
Minimum - Maximum-0.072024755 - 0.11736728
Average (Standard dev.)-0.0000347507 (±0.00861495)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions969696
Spacing969696
CellA=B=C: 321.984 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: half map A

Fileemd_70491_half_map_1.map
Annotationhalf map A
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Half map: half map B

Fileemd_70491_half_map_2.map
Annotationhalf map B
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : BG505 GT1.1 SOSIP in complex with V1V2V3 epitope polyclonal antib...

EntireName: BG505 GT1.1 SOSIP in complex with V1V2V3 epitope polyclonal antibodies isolated from a participant in the IAVI C101 clinical trial
Components
  • Complex: BG505 GT1.1 SOSIP in complex with V1V2V3 epitope polyclonal antibodies isolated from a participant in the IAVI C101 clinical trial

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Supramolecule #1: BG505 GT1.1 SOSIP in complex with V1V2V3 epitope polyclonal antib...

SupramoleculeName: BG505 GT1.1 SOSIP in complex with V1V2V3 epitope polyclonal antibodies isolated from a participant in the IAVI C101 clinical trial
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

Concentration0.03 mg/mL
BufferpH: 7.4
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 F20
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: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Tecnai F20 / 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 coordinates converted to map using UCSF ChimeraX molmap and low pass filtered to 40 A
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 / Number images used: 3153
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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