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- EMDB-42907: sRT-V2t NFL trimer in complex with 12CA5 Fab and RM20A3 Fab -

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Basic information

Entry
Database: EMDB / ID: EMD-42907
TitlesRT-V2t NFL trimer in complex with 12CA5 Fab and RM20A3 Fab
Map datamain map
Sample
  • Complex: sRT-V2t NFL trimer in complex with 12CA5 Fab
KeywordsHIV Env / HA tag / NFL trimer / VIRAL PROTEIN-IMMUNE SYSTEM complex
Biological speciesHuman immunodeficiency virus 1
Methodsingle particle reconstruction / negative staining / Resolution: 32.0 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_42907.png

Downloads & links

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Map

FileDownload / File: emd_42907.map.gz / Format: CCP4 / Size: 42.9 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.)
1.98 Å/pix.
x 224 pix.
= 443.52 Å		1.98 Å/pix.
x 224 pix.
= 443.52 Å		1.98 Å/pix.
x 224 pix.
= 443.52 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.98 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.015
Minimum - Maximum-0.029513279 - 0.103361614
Average (Standard dev.)0.000057704365 (±0.0037406923)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions224224224
Spacing224224224
CellA=B=C: 443.52002 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: half map A

Fileemd_42907_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_42907_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 : sRT-V2t NFL trimer in complex with 12CA5 Fab

EntireName: sRT-V2t NFL trimer in complex with 12CA5 Fab
Components
  • Complex: sRT-V2t NFL trimer in complex with 12CA5 Fab

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Supramolecule #1: sRT-V2t NFL trimer in complex with 12CA5 Fab

SupramoleculeName: sRT-V2t NFL trimer in complex with 12CA5 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
GridModel: Homemade / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Pretreatment - Type: GLOW DISCHARGE

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Electron microscopy

MicroscopeTFS TALOS
Image recordingFilm or detector model: FEI CETA (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: SIDE ENTRY, EUCENTRIC

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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: 32.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: RELION (ver. 4) / Number images used: 1735
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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