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- EMDB-42913: sRT-V4 NFL trimer in complex with 12CA5 Fab and RM20A3 Fab -

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Basic information

Entry
Database: EMDB / ID: EMD-42913
TitlesRT-V4 NFL trimer in complex with 12CA5 Fab and RM20A3 Fab
Map datamain map (class 1)
Sample
  • Complex: sRT-V4 NFL trimer in complex with 12CA5 Fab and RM20A3 Fab
KeywordsHIV Env / HA tag / NFL trimer / VIRAL PROTEIN-IMMUNE SYSTEM complex
Biological speciesHuman immunodeficiency virus 1
Methodsingle particle reconstruction / negative staining / Resolution: 33.0 Å
AuthorsLee W-H / Ozorowski G / Ward AB
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)UM1 AI144462 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI136621-05 United States
CitationJournal: Cell Rep / Year: 2025
Title: Molecular parameters governing antibody FcγR signaling and effector functions in the context of HIV envelope.
Authors: Michael V Bick / Eduard Puig / David Beauparlant / Rebecca Nedellec / Iszac Burton / Keihvan Ardaghi / Thea R Zalunardo / Raiza Bastidas / Xuduo Li / Javier Guenaga / Wen-Hsin Lee / Richard ...Authors: Michael V Bick / Eduard Puig / David Beauparlant / Rebecca Nedellec / Iszac Burton / Keihvan Ardaghi / Thea R Zalunardo / Raiza Bastidas / Xuduo Li / Javier Guenaga / Wen-Hsin Lee / Richard Wyatt / Wenwen Zhu / Max Crispin / Gabriel Ozorowski / Andrew B Ward / Dennis R Burton / Lars Hangartner /
Abstract: Antibody effector functions contribute to the immune response to pathogens and can influence the efficacy of antibodies as therapeutics. To date, however, there is limited information on the ...Antibody effector functions contribute to the immune response to pathogens and can influence the efficacy of antibodies as therapeutics. To date, however, there is limited information on the molecular parameters that govern fragment crystallizable (Fc) effector functions. In this study, using AI-assisted protein design, the influences of binding kinetics, epitope location, and stoichiometry of binding on cellular Fc effector functions were investigated using engineered HIV-1 envelope as a model antigen. For this antigen, stoichiometry of binding was found to be the primary molecular determinant of FcγRIIIa signaling, antibody-dependent cellular cytotoxicity, and antibody-dependent cellular phagocytosis, while epitope location and antibodybinding kinetics, at least in the ranges investigated, were of no substantial impact. These findings are of importance for informing the development of vaccination strategies against HIV-1 and, possibly, other viral pathogens.
History
DepositionNov 22, 2023-
Header (metadata) releaseDec 11, 2024-
Map releaseDec 11, 2024-
UpdateApr 16, 2025-
Current statusApr 16, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_42913.png

Downloads & links

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Map

FileDownload / File: emd_42913.map.gz / Format: CCP4 / Size: 27 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationmain map (class 1)
Projections & slices

Image control

Size
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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: 0.028
Minimum - Maximum-0.030261263 - 0.09829411
Average (Standard dev.)0.0002609061 (±0.004614694)
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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Additional map: additional map 1 (class 2)

Fileemd_42913_additional_1.map
Annotationadditional map 1 (class 2)
Projections & Slices
AxesZYX

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Additional map: additional map 2 (class 3)

Fileemd_42913_additional_2.map
Annotationadditional map 2 (class 3)
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Half map: half map A

Fileemd_42913_half_map_1.map
Annotationhalf map A
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map B

Fileemd_42913_half_map_2.map
Annotationhalf map B
Projections & Slices
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Histogram

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Sample components

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Entire : sRT-V4 NFL trimer in complex with 12CA5 Fab and RM20A3 Fab

EntireName: sRT-V4 NFL trimer in complex with 12CA5 Fab and RM20A3 Fab
Components
  • Complex: sRT-V4 NFL trimer in complex with 12CA5 Fab and RM20A3 Fab

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Supramolecule #1: sRT-V4 NFL trimer in complex with 12CA5 Fab and RM20A3 Fab

SupramoleculeName: sRT-V4 NFL trimer in complex with 12CA5 Fab and RM20A3 Fab
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Human immunodeficiency virus 1

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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

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Electron microscopy

MicroscopeFEI TECNAI SPIRIT
Image recordingFilm or detector model: FEI EAGLE (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
Sample stageSpecimen holder model: SIDE ENTRY, EUCENTRIC
Experimental equipment
Model: Tecnai Spirit / Image courtesy: FEI Company

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Image processing

Startup modelType of model: EMDB MAP
EMDB ID:

20396


Details: low pass filtered to 40 Angstrom
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 33.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: RELION (ver. 4) / Number images used: 1774
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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