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- EMDB-70470: BG505 MD39.3 Env gp151 MPER nanodisc in complex with 10E8, BG18 a... -

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Basic information

Entry
Database: EMDB / ID: EMD-70470
TitleBG505 MD39.3 Env gp151 MPER nanodisc in complex with 10E8, BG18 and VRC01 Fabs (2x 10E8 Fabs)
Map datasharpened map
Sample
  • Complex: BG505 MD39.3 Env gp151 MPER nanodisc in complex with 10E8, BG18 and VRC01 Fabs (2x 10E8 Fabs)
KeywordsMPER / HIV-1 / broadly neutralizing antibody / VIRAL PROTEIN
Biological speciesHuman immunodeficiency virus 1
Methodsingle particle reconstruction / cryo EM / Resolution: 4.3 Å
AuthorsRantalainen K / Ozorowski G / Gharpure A / Ward AB
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)UM1 AI144462 United States
CitationJournal: bioRxiv / Year: 2025
Title: Virus glycoprotein nanodisc platform for vaccine design.
Authors: Kimmo Rantalainen / Alessia Liguori / Gabriel Ozorowski / Claudia Flynn / Jon M Steichen / Olivia Swanson / Patrick J Madden / Sabyasachi Baboo / Swastik Phulera / Anant Gharpure / Danny Lu ...Authors: Kimmo Rantalainen / Alessia Liguori / Gabriel Ozorowski / Claudia Flynn / Jon M Steichen / Olivia Swanson / Patrick J Madden / Sabyasachi Baboo / Swastik Phulera / Anant Gharpure / Danny Lu / Oleksandr Kalyuzhniy / Patrick Skog / Sierra Terada / Monolina Shil / Jolene K Diedrich / Erik Georgeson / Ryan Tingle / Saman Eskandarzadeh / Wen-Hsin Lee / Nushin Alavi / Diana Goodwin / Michael Kubitz / Sonya Amirzehni / Sunny Himansu / Devin Sok / Jeong Hyun Lee / John R Yates / James C Paulson / Shane Crotty / Torben Schiffner / Andrew B Ward / William R Schief /
Abstract: Transmembrane glycoproteins of enveloped viruses are the targets of neutralizing antibodies and essential vaccine antigens. mRNA-LNP technology allows in situ production of transmembrane ...Transmembrane glycoproteins of enveloped viruses are the targets of neutralizing antibodies and essential vaccine antigens. mRNA-LNP technology allows in situ production of transmembrane glycoproteins upon immunization, but biophysical characterization of transmembrane antigens and in vitro analysis of post-immunization antibody responses typically rely on soluble proteins. Here, we present a methodological platform for assembling transmembrane glycoprotein vaccine candidates into lipid nanodiscs. We demonstrate the utility of the nanodiscs in HIV membrane proximal external region (MPER)-targeting vaccine development by binding assays using surface plasmon resonance (SPR), ex vivo B cell sorting with fluorescence-activated cell sorting (FACS), and by determining the structure of a prototypical HIV MPER-targeting immunogen nanodisc in complex with three broadly neutralizing antibodies (bnAbs), including the MPER bnAb 10E8, to 3.5 Å by cryogenic electron microscopy (cryo-EM), providing a template for structure-based immunogen design for MPER. Overall, the platform offers a tool for accelerating the development of next-generation viral vaccines.
History
DepositionMay 1, 2025-
Header (metadata) releaseJul 30, 2025-
Map releaseJul 30, 2025-
UpdateJul 30, 2025-
Current statusJul 30, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_70470.png

Downloads & links

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Map

FileDownload / File: emd_70470.map.gz / Format: CCP4 / Size: 600.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationsharpened map
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.72 Å/pix.
x 540 pix.
= 387.72 Å		0.72 Å/pix.
x 540 pix.
= 387.72 Å		0.72 Å/pix.
x 540 pix.
= 387.72 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.718 Å
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Histogram (log scale)
Contour LevelBy AUTHOR: 0.05
Minimum - Maximum-0.09717934 - 0.16167456
Average (Standard dev.)-0.000086934306 (±0.007511644)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions540540540
Spacing540540540
CellA=B=C: 387.72 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_70470_msk_1.map
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Half map: half map A

Fileemd_70470_half_map_1.map
Annotationhalf map A
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Half map: half map B

Fileemd_70470_half_map_2.map
Annotationhalf map B
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Sample components

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Entire : BG505 MD39.3 Env gp151 MPER nanodisc in complex with 10E8, BG18 a...

EntireName: BG505 MD39.3 Env gp151 MPER nanodisc in complex with 10E8, BG18 and VRC01 Fabs (2x 10E8 Fabs)
Components
  • Complex: BG505 MD39.3 Env gp151 MPER nanodisc in complex with 10E8, BG18 and VRC01 Fabs (2x 10E8 Fabs)

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Supramolecule #1: BG505 MD39.3 Env gp151 MPER nanodisc in complex with 10E8, BG18 a...

SupramoleculeName: BG505 MD39.3 Env gp151 MPER nanodisc in complex with 10E8, BG18 and VRC01 Fabs (2x 10E8 Fabs)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Human immunodeficiency virus 1

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration8 mg/mL
BufferpH: 7.4
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 400 / Support film - Material: GRAPHENE OXIDE / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Average electron dose: 45.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 190000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL / In silico model: ab initio reconstruction from cryoSPARC
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 7964
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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