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- EMDB-22163: AMC018 SOSIPv4.2 in complex with mAb RI808 -

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Basic information

Entry
Database: EMDB / ID: EMD-22163
TitleAMC018 SOSIPv4.2 in complex with mAb RI808
Map dataAMC018 SOSIPv4.2 in complex with mAb RI808
Sample
  • Complex: AMC018 SOSIPv4.2 in complex with mAb RI808
    • Complex: AMC018 SOSIPv4.2
    • Complex: mAb RI808
Biological speciesHuman immunodeficiency virus 1 / unidentified (others)
Methodsingle particle reconstruction / negative staining / Resolution: 26.0 Å
AuthorsCottrell CA / Copps J / Ward AB
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)Al131873 United States
CitationJournal: Cell Rep / Year: 2021
Title: Mining HIV controllers for broad and functional antibodies to recognize and eliminate HIV-infected cells.
Authors: Evan D Rossignol / Anne-Sophie Dugast / Hacheming Compere / Christopher A Cottrell / Jeffrey Copps / Shu Lin / Deniz Cizmeci / Michael S Seaman / Margaret E Ackerman / Andrew B Ward / Galit Alter / Boris Julg /
Abstract: HIV monoclonal antibodies for viral reservoir eradication strategies will likely need to recognize reactivated infected cells and potently drive Fc-mediated innate effector cell activity. We ...HIV monoclonal antibodies for viral reservoir eradication strategies will likely need to recognize reactivated infected cells and potently drive Fc-mediated innate effector cell activity. We systematically characterize a library of 185 HIV-envelope-specific antibodies derived from 15 spontaneous HIV controllers (HCs) that selectively exhibit robust serum Fc functionality and compared them to broadly neutralizing antibodies (bNAbs) in clinical development. Within the 10 antibodies with the broadest cell-recognition capability, seven originated from HCs and three were bNAbs. V3-loop-targeting antibodies are enriched among the top cell binders, suggesting the V3-loop may be selectively exposed and accessible on the cell surface. Fc functionality is more variable across antibodies, which is likely influenced by distinct binding topology and corresponding Fc accessibility, highlighting not only the importance of target-cell recognition but also the need to optimize for Fc-mediated elimination. Ultimately, our results demonstrate that this comprehensive selection process can identify monoclonal antibodies poised to eliminate infected cells.
History
DepositionJun 15, 2020-
Header (metadata) releaseMay 26, 2021-
Map releaseMay 26, 2021-
UpdateDec 8, 2021-
Current statusDec 8, 2021Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.016
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.016
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_22163.png

Downloads & links

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Map

FileDownload / File: emd_22163.map.gz / Format: CCP4 / Size: 15.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationAMC018 SOSIPv4.2 in complex with mAb RI808
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.98 Å/pix.
x 160 pix.
= 316.8 Å		1.98 Å/pix.
x 160 pix.
= 316.8 Å		1.98 Å/pix.
x 160 pix.
= 316.8 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: 0.016 / Movie #1: 0.016
Minimum - Maximum-0.04676209 - 0.08692603
Average (Standard dev.)0.00023820109 (±0.00631072)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions160160160
Spacing160160160
CellA=B=C: 316.8 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.981.981.98
M x/y/z160160160
origin x/y/z0.0000.0000.000
length x/y/z316.800316.800316.800
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS160160160
D min/max/mean-0.0470.0870.000

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Supplemental data

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Sample components

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Entire : AMC018 SOSIPv4.2 in complex with mAb RI808

EntireName: AMC018 SOSIPv4.2 in complex with mAb RI808
Components
  • Complex: AMC018 SOSIPv4.2 in complex with mAb RI808
    • Complex: AMC018 SOSIPv4.2
    • Complex: mAb RI808

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Supramolecule #1: AMC018 SOSIPv4.2 in complex with mAb RI808

SupramoleculeName: AMC018 SOSIPv4.2 in complex with mAb RI808 / type: complex / ID: 1 / Parent: 0

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Supramolecule #2: AMC018 SOSIPv4.2

SupramoleculeName: AMC018 SOSIPv4.2 / type: complex / ID: 2 / Parent: 1
Source (natural)Organism: Human immunodeficiency virus 1
Recombinant expressionOrganism: Homo sapiens (human) / Recombinant cell: HEK293F

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Supramolecule #3: mAb RI808

SupramoleculeName: mAb RI808 / type: complex / ID: 3 / Parent: 1
Source (natural)Organism: unidentified (others)

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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

BufferpH: 7.4
StainingType: NEGATIVE / Material: Uranyl Formate
GridDetails: unspecified

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
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 opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm
Sample stageSpecimen holder model: SIDE ENTRY, EUCENTRIC
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 26.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 7954
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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