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- EMDB-70847: Rabbit 37450 base, gp41-FP and gp120int epitope polyclonal Fabs i... -

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Basic information

Entry
Database: EMDB / ID: EMD-70847
TitleRabbit 37450 base, gp41-FP and gp120int epitope polyclonal Fabs in complex with BG505 MD39.3 SOSIP
Map datamain map
Sample
  • Complex: Rabbit 37496 base and V1/V3 epitope polyclonal Fabs in complex with BG505 MD39.3 SOSIP
    • Complex: HIV-1 Env BG505 MD39.3 SOSIP gp140
    • Complex: rabbit polyclonal Fabs
KeywordsHIV-1 / Env / EMPEM / VIRAL PROTEIN
Biological speciesHuman immunodeficiency virus 1 / Oryctolagus cuniculus (rabbit)
Methodsingle particle reconstruction / negative staining / Resolution: 25.0 Å
AuthorsOzorowski G / Torres JL / Jackson AM / Ward AB
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)UM1AI144462 United States
CitationJournal: Sci Transl Med / Year: 2025
Title: Vaccination with an mRNA-encoded membrane-bound HIV envelope trimer induces neutralizing antibodies in animal models.
Authors: Parham Ramezani-Rad / Christopher A Cottrell / Ester Marina-Zárate / Alessia Liguori / Elise Landais / Jonathan L Torres / Amber Myers / Jeong Hyun Lee / Sabyasachi Baboo / Claudia Flynn / ...Authors: Parham Ramezani-Rad / Christopher A Cottrell / Ester Marina-Zárate / Alessia Liguori / Elise Landais / Jonathan L Torres / Amber Myers / Jeong Hyun Lee / Sabyasachi Baboo / Claudia Flynn / Katherine McKenney / Eugenia Salcedo / Xiaoya Zhou / Oleksandr Kalyuzhniy / Erik Georgeson / Nicole Phelps / Danny Lu / Saman Eskandarzadeh / Sergey Menis / Michael Kubitz / Bettina Groschel / Nushin Alavi / Abigail M Jackson / Wen-Hsin Lee / Andy S Tran / Elana Ben-Akiva / Katarzyna Kaczmarek Michaels / Jolene K Diedrich / Chiamaka A Enemuo / Vanessa Lewis / Arpan Pradhan / Sudhir Pai Kasturi / Torben Schiffner / Jon M Steichen / Diane G Carnathan / Sunny Himansu / John R Yates / James C Paulson / Gabriel Ozorowski / Darrell J Irvine / Guido Silvestri / Devin Sok / Andrew B Ward / Shane Crotty / William R Schief /
Abstract: A protective vaccine against human immunodeficiency virus (HIV) will likely need to induce broadly neutralizing antibodies (bnAbs) that engage relatively conserved epitopes on the HIV envelope ...A protective vaccine against human immunodeficiency virus (HIV) will likely need to induce broadly neutralizing antibodies (bnAbs) that engage relatively conserved epitopes on the HIV envelope glycoprotein (Env) trimer. Nearly all vaccine strategies to induce bnAbs require the use of complex immunization regimens involving a series of different immunogens, most of which are Env trimers. Producing protein-based clinical material to evaluate such relatively complex regimens in humans presents major challenges in cost and time. Furthermore, immunization with HIV trimers as soluble proteins induces strong nonneutralizing responses to the trimer base, which is normally occluded on the virion. These base responses could potentially detract from the elicitation of nAbs and the eventual induction of bnAbs. mRNA vaccine platforms offer potential advantages over protein delivery for HIV vaccine development, including increased production speed, reduced cost, and the ability to deliver membrane-bound trimers that might facilitate improved immuno-focusing to nonbase epitopes. We report the design of mRNA-delivered soluble and membrane-bound forms of a stabilized native-like Env trimer (BG505 MD39.3); initial immunogenicity evaluation in rabbits that triggered clinical evaluation; and more comprehensive evaluation of B cell, T cell, and antibody responses in nonhuman primates. mRNA-encoded membrane-bound Env immunization elicited reduced off-target base-directed Env responses and stronger nAb responses compared with mRNA-encoded soluble Env. Overall, mRNA delivery of membrane-bound Env appears promising for enhancing B cell responses to subdominant epitopes and facilitating rapid translation to clinical testing, which should assist HIV vaccine development.
History
DepositionMay 27, 2025-
Header (metadata) releaseAug 13, 2025-
Map releaseAug 13, 2025-
UpdateAug 13, 2025-
Current statusAug 13, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_70847.png

Downloads & links

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Map

FileDownload / File: emd_70847.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

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.06 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.02
Minimum - Maximum-0.037687283 - 0.11291413
Average (Standard dev.)0.00022212621 (±0.005072921)
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 A

Fileemd_70847_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_70847_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 : Rabbit 37496 base and V1/V3 epitope polyclonal Fabs in complex wi...

EntireName: Rabbit 37496 base and V1/V3 epitope polyclonal Fabs in complex with BG505 MD39.3 SOSIP
Components
  • Complex: Rabbit 37496 base and V1/V3 epitope polyclonal Fabs in complex with BG505 MD39.3 SOSIP
    • Complex: HIV-1 Env BG505 MD39.3 SOSIP gp140
    • Complex: rabbit polyclonal Fabs

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Supramolecule #1: Rabbit 37496 base and V1/V3 epitope polyclonal Fabs in complex wi...

SupramoleculeName: Rabbit 37496 base and V1/V3 epitope polyclonal Fabs in complex with BG505 MD39.3 SOSIP
type: complex / ID: 1 / Parent: 0

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Supramolecule #2: HIV-1 Env BG505 MD39.3 SOSIP gp140

SupramoleculeName: HIV-1 Env BG505 MD39.3 SOSIP gp140 / type: complex / ID: 2 / Parent: 1
Source (natural)Organism: Human immunodeficiency virus 1

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Supramolecule #3: rabbit polyclonal Fabs

SupramoleculeName: rabbit polyclonal Fabs / type: complex / ID: 3 / Parent: 1
Source (natural)Organism: Oryctolagus cuniculus (rabbit)

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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 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: 2.0 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 coordinates converted to map using molmap in UCSF Chimera and low pass filtered to 40 A
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 25.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: RELION (ver. 4.0) / Number images used: 6153
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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