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- EMDB-28120: DH272.2 Fab in Complex with CH848 TF DS SOSIP Env -

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Basic information

Entry
Database: EMDB / ID: EMD-28120
TitleDH272.2 Fab in Complex with CH848 TF DS SOSIP Env
Map dataDH272.2 Fab bound to CH848 TF DS SOSIP Env
Sample
  • Complex: Complex between DH272.2 Fab and CH848 TF DS SOSIP Env
    • Complex: DH272.2 Fab
    • Complex: CH848 TF DS SOSIP Env
Biological speciesHomo sapiens (human) / Human immunodeficiency virus
Methodsingle particle reconstruction / negative staining / Resolution: 14.35 Å
AuthorsFera D
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)1R15AI150484 United States
CitationJournal: Front Immunol / Year: 2022
Title: Analysis of two cooperating antibodies unveils immune pressure imposed on HIV Env to elicit a V3-glycan supersite broadly neutralizing antibody lineage.
Authors: Maxwell T Finkelstein / Emma Parker Miller / Molly C Erdman / Daniela Fera /
Abstract: Elicitation of broadly neutralizing antibodies (bnAbs) is a goal of vaccine design as a strategy for targeting highly divergent strains of HIV-1. Current HIV-1 vaccine design efforts seek to elicit ...Elicitation of broadly neutralizing antibodies (bnAbs) is a goal of vaccine design as a strategy for targeting highly divergent strains of HIV-1. Current HIV-1 vaccine design efforts seek to elicit bnAbs by first eliciting their precursors through prime-boost regimens. This requires an understanding of the co-evolution between viruses and antibodies. Towards this goal, we have analyzed two cooperating antibodies, DH475 and DH272, which exerted pressure on the HIV population in an infected donor, called CH848, to evolve in such a way that it became sensitive to the V3-glycan supersite DH270 bnAb lineage. We obtained a 2.90Å crystal structure of DH475 in complex with the Man glycan and a negative stain EM model of DH272 in complex with the HIV-1 spike trimer, Env. Coupled with additional modeling studies and biochemical data, our studies reveal that DH475 contacts a V3- and V4-glycan dependent epitope accessible on an open or shed Env and that DH272 makes critical contacts with the V1V2 and V3 loops on HIV-1 Env. Using these data, we suggest a prime-boost regimen that may facilitate the initiation of DH270-like bnAb precursors.
History
DepositionSep 12, 2022-
Header (metadata) releaseSep 21, 2022-
Map releaseSep 21, 2022-
UpdateOct 26, 2022-
Current statusOct 26, 2022Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_28120.png

Downloads & links

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Map

FileDownload / File: emd_28120.map.gz / Format: CCP4 / Size: 28.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationDH272.2 Fab bound to CH848 TF DS SOSIP Env
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
3 Å/pix.
x 196 pix.
= 588. Å		3 Å/pix.
x 196 pix.
= 588. Å		3 Å/pix.
x 196 pix.
= 588. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 3 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.51
Minimum - Maximum-0.9839587 - 3.2509463
Average (Standard dev.)-0.017725587 (±0.14556414)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions196196196
Spacing196196196
CellA=B=C: 588.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: DH272.2 Fab bound to CH848 TF DS SOSIP Env

Fileemd_28120_half_map_1.map
AnnotationDH272.2 Fab bound to CH848 TF DS SOSIP Env
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: DH272.2 Fab bound to CH848 TF DS SOSIP Env

Fileemd_28120_half_map_2.map
AnnotationDH272.2 Fab bound to CH848 TF DS SOSIP Env
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Complex between DH272.2 Fab and CH848 TF DS SOSIP Env

EntireName: Complex between DH272.2 Fab and CH848 TF DS SOSIP Env
Components
  • Complex: Complex between DH272.2 Fab and CH848 TF DS SOSIP Env
    • Complex: DH272.2 Fab
    • Complex: CH848 TF DS SOSIP Env

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Supramolecule #1: Complex between DH272.2 Fab and CH848 TF DS SOSIP Env

SupramoleculeName: Complex between DH272.2 Fab and CH848 TF DS SOSIP Env / type: complex / Chimera: Yes / ID: 1 / Parent: 0

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Supramolecule #2: DH272.2 Fab

SupramoleculeName: DH272.2 Fab / type: complex / Chimera: Yes / ID: 2 / Parent: 1
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human) / Recombinant cell: HEK-293T

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Supramolecule #3: CH848 TF DS SOSIP Env

SupramoleculeName: CH848 TF DS SOSIP Env / type: complex / Chimera: Yes / ID: 3 / Parent: 1
Source (natural)Organism: Human immunodeficiency virus
Recombinant expressionOrganism: Homo sapiens (human) / Recombinant cell: HEK293S GnTi-

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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: 7.5
StainingType: NEGATIVE / Material: Uranyl Formate

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Electron microscopy

MicroscopeFEI TECNAI F20
Image recordingFilm or detector model: OTHER / 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: 3.0 µm / Nominal defocus min: 3.0 µm
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 14.35 Å / Resolution method: FSC 0.5 CUT-OFF / Number images used: 19124
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE

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