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- EMDB-49656: Rabbit RB142 polyclonal Fab in complex with HIV-1 1086C NFL Env trimer -

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Basic information

Entry
Database: EMDB / ID: EMD-49656
TitleRabbit RB142 polyclonal Fab in complex with HIV-1 1086C NFL Env trimer
Map datamain map
Sample
  • Complex: Rabbit RB142 polyclonal Fab in complex with HIV-1 1086C NFL Env trimer
KeywordsEMPEM / HIV / vaccine / VLP / VIRAL PROTEIN
Biological speciesOryctolagus cuniculus (rabbit)
Methodsingle particle reconstruction / negative staining / Resolution: 15.0 Å
AuthorsLin RN / Torres JL / Ozorowski G / Ward AB
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)P01 AI157299 United States
CitationJournal: Nat Commun / Year: 2025
Title: Antigen persistence and TLR stimulation contribute to induction of a durable HIV-1-specific neutralizing antibody response.
Authors: Kenta Matsuda / Mitra Harrison / Eleanor Wettstein / Jessica Pederson / Alyssa A Pullano / Lyuba Bolkhovitinov / Breanna Kim / Isabel Steinberg / Trevor Griesman / Sarah Stuccio / Daniel ...Authors: Kenta Matsuda / Mitra Harrison / Eleanor Wettstein / Jessica Pederson / Alyssa A Pullano / Lyuba Bolkhovitinov / Breanna Kim / Isabel Steinberg / Trevor Griesman / Sarah Stuccio / Daniel Rogan / Andy Patamawenu / Tulley Shofner / Nathaniel E Wright / Jonathan D Webber / Freya Van't Veer / Rachel Roenicke / Emma Koory / Peyton M Roeder / Ellison Ober / Benjamin Leach / Yaroslav Tsybovsky / Tyler Stephens / Ivan Del Moral-Sanchez / Ilja Bontjer / Lori W McGinnes-Cullen / Eric Chu / Jason Liang / Jonathan L Torres / Ryan N Lin / Andy S Tran / Gabrielle Dziubla / Leonid Serebryannyy / Sandeep Narpala / Bob Lin / Mike Castro / Gabriel Ozorowski / Andrew B Ward / Rogier W Sanders / Peter D Kwong / Javier Guenaga / Richard Wyatt / Trudy Morrison / Mark Connors /
Abstract: HIV-1 Env glycoprotein (Env) immunogenicity is limited in part by structural instability and extensive glycan shielding and is likely the greatest obstacle to an HIV-1 vaccine. Stabilized Env trimers ...HIV-1 Env glycoprotein (Env) immunogenicity is limited in part by structural instability and extensive glycan shielding and is likely the greatest obstacle to an HIV-1 vaccine. Stabilized Env trimers can elicit serum neutralizing antibodies, but the response is short-lived. Here we use Newcastle Disease Virus-like particle (NDV-VLP) platform to present stabilized versions of HIV-1 Env at high valency and in the context of varied conformational stability, adjuvants, dose, and antigen persistence. Influenza virus hemagglutinin, or SARS-CoV2 Spike-bearing VLPs rapidly induce neutralizing antibodies, in contrast, they were not induced by those bearing Env. A replicating adenovirus type 4 expressing Env rapidly induces autologous neutralizing antibodies. However, durable neutralizing antibodies are induced only when multiple features of a replicating virus infection are combined, with the largest impact from dose and escalating dose. In summary, we show here immunogenicity of HIV-1 Env could be improved by reproducing features of virus infection.
History
DepositionMar 12, 2025-
Header (metadata) releaseMar 26, 2025-
Map releaseMar 26, 2025-
UpdateJun 25, 2025-
Current statusJun 25, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_49656.png

Downloads & links

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Map

FileDownload / File: emd_49656.map.gz / Format: CCP4 / Size: 3.4 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.)
3.78 Å/pix.
x 96 pix.
= 362.88 Å		3.78 Å/pix.
x 96 pix.
= 362.88 Å		3.78 Å/pix.
x 96 pix.
= 362.88 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 3.78 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.02
Minimum - Maximum-0.061546247 - 0.11639508
Average (Standard dev.)0.00006255002 (±0.0050339308)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions969696
Spacing969696
CellA=B=C: 362.88 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: half map B

Fileemd_49656_half_map_1.map
Annotationhalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map A

Fileemd_49656_half_map_2.map
Annotationhalf map A
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 RB142 polyclonal Fab in complex with HIV-1 1086C NFL Env trimer

EntireName: Rabbit RB142 polyclonal Fab in complex with HIV-1 1086C NFL Env trimer
Components
  • Complex: Rabbit RB142 polyclonal Fab in complex with HIV-1 1086C NFL Env trimer

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Supramolecule #1: Rabbit RB142 polyclonal Fab in complex with HIV-1 1086C NFL Env trimer

SupramoleculeName: Rabbit RB142 polyclonal Fab in complex with HIV-1 1086C NFL Env trimer
type: complex / ID: 1 / Parent: 0
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 / Details: 2% uranyl formate applied for 45 s
GridModel: Homemade / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: FEI FALCON IV (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: 2.0 µm / Nominal defocus min: 1.0 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER

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Image processing

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

6v0r


Details: coordinates converted to map using ChimeraX molmap and low pass filtered to 40 A
Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 15.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: RELION (ver. 4.0) / Number images used: 114209
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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