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- EMDB-43910: nsEM of HIV-1 CH505/BG505 SOSIP.v8.1 Env in Complex with Week 6 B... -

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Basic information

Entry
Database: EMDB / ID: EMD-43910
TitlensEM of HIV-1 CH505/BG505 SOSIP.v8.1 Env in Complex with Week 6 Base Epitope pAb (Rabbit ID: 2474)
Map data
Sample
  • Complex: nsEM of HIV-1 CH505/BG505 SOSIP.v8.1 Env in Complex with Week 6 Base Epitope pAb (Rabbit ID: 2474)
    • Complex: Rabbit Polyclonal Antibody - Base Epitope
      • Protein or peptide: HIV-1 CH505/BG505 SOSIP.v8.1 - gp140
    • Complex: HIV-1 CH505/BG505 SOSIP.v8.1 Env
KeywordsHIV / Polyclonal / Antibodies / nsEMPEM / Rabbit / VIRAL PROTEIN
Biological speciesOryctolagus cuniculus (rabbit) / Human immunodeficiency virus 1
Methodsingle particle reconstruction / negative staining / Resolution: 25.0 Å
AuthorsBrown S / Ward AB
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI136621 United States
Bill & Melinda Gates FoundationINV-002916 United States
CitationJournal: Sci Immunol / Year: 2025
Title: Anti-immune complex antibodies are elicited during repeated immunization with HIV Env immunogens.
Authors: Sharidan Brown / Aleksandar Antanasijevic / Leigh M Sewall / Daniel Montiel Garcia / James Ferguson / Philip J M Brouwer / Rogier W Sanders / Andrew B Ward /
Abstract: Vaccination strategies against HIV-1 aim to elicit broadly neutralizing antibodies (bnAbs) using prime-boost regimens with HIV envelope (Env) immunogens. Epitope mapping has shown that early antibody ...Vaccination strategies against HIV-1 aim to elicit broadly neutralizing antibodies (bnAbs) using prime-boost regimens with HIV envelope (Env) immunogens. Epitope mapping has shown that early antibody responses are directed to easily accessible nonneutralizing epitopes on Env instead of bnAb epitopes. Autologously neutralizing antibody responses appear upon boosting, once immunodominant epitopes are saturated. Here, we use electron microscopy-based polyclonal epitope mapping (EMPEM) to elucidate how repeated immunization with HIV Env SOSIP immunogens results in the generation of Ab2α anti-idiotypic antibodies in rabbits and rhesus macaques. We present the structures of six anti-immune complex antibodies and find that they target idiotopes composed of framework regions of antibodies bound to Env. Examination of cryo-electron microscopy density enabled prediction of sequences for an anti-immune complex antibody, the paratope of which is enriched with aromatic amino acids. This work sheds light on current vaccine development efforts for HIV, as well as for other pathogens in which repeated exposure to antigen is required.
History
DepositionMar 4, 2024-
Header (metadata) releaseJul 2, 2025-
Map releaseJul 2, 2025-
UpdateJul 2, 2025-
Current statusJul 2, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_43910.png

Downloads & links

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Map

FileDownload / File: emd_43910.map.gz / Format: CCP4 / Size: 42.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1.77 Å/pix.
x 224 pix.
= 396.48 Å		1.77 Å/pix.
x 224 pix.
= 396.48 Å		1.77 Å/pix.
x 224 pix.
= 396.48 Å

Surface

Projections

Slices (1/3)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.77 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.015
Minimum - Maximum-0.02527492 - 0.06912728
Average (Standard dev.)0.00008144817 (±0.0030115768)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions224224224
Spacing224224224
CellA=B=C: 396.47998 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_43910_half_map_1.map
Projections & Slices
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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_43910_half_map_2.map
Projections & Slices
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Histogram (log scale)

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Sample components

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Entire : nsEM of HIV-1 CH505/BG505 SOSIP.v8.1 Env in Complex with Week 6 B...

EntireName: nsEM of HIV-1 CH505/BG505 SOSIP.v8.1 Env in Complex with Week 6 Base Epitope pAb (Rabbit ID: 2474)
Components
  • Complex: nsEM of HIV-1 CH505/BG505 SOSIP.v8.1 Env in Complex with Week 6 Base Epitope pAb (Rabbit ID: 2474)
    • Complex: Rabbit Polyclonal Antibody - Base Epitope
      • Protein or peptide: HIV-1 CH505/BG505 SOSIP.v8.1 - gp140
    • Complex: HIV-1 CH505/BG505 SOSIP.v8.1 Env

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Supramolecule #1: nsEM of HIV-1 CH505/BG505 SOSIP.v8.1 Env in Complex with Week 6 B...

SupramoleculeName: nsEM of HIV-1 CH505/BG505 SOSIP.v8.1 Env in Complex with Week 6 Base Epitope pAb (Rabbit ID: 2474)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2

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Supramolecule #2: Rabbit Polyclonal Antibody - Base Epitope

SupramoleculeName: Rabbit Polyclonal Antibody - Base Epitope / type: complex / ID: 2 / Parent: 1 / Macromolecule list: all
Source (natural)Organism: Oryctolagus cuniculus (rabbit)

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Supramolecule #3: HIV-1 CH505/BG505 SOSIP.v8.1 Env

SupramoleculeName: HIV-1 CH505/BG505 SOSIP.v8.1 Env / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2
Details: Chimeric antigen composed of CH505 and BG505 HIV-1 strains.
Source (natural)Organism: Human immunodeficiency virus 1

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Macromolecule #1: HIV-1 CH505/BG505 SOSIP.v8.1 - gp140

MacromoleculeName: HIV-1 CH505/BG505 SOSIP.v8.1 - gp140 / type: protein_or_peptide / ID: 1
Details: The sequence contains engineered SOSIP mutations. This is a chimeric antigen composed of CH505 and BG505 HIV-1 strains.
Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MDAMKRGLCC VLLLCGAVFV SPSQEIHARF RRGARAENLW VTVYYGVPVW KDAETTLFCA SDAKAYETEK RNVWATHCCV PTDPNPQEIH LENVTEEFNM WKNNMVEQMH EDIISLWDQS LKPCVKLTPL CVTLNCTNAT ASNSSIIEGM KNCSFNITTE LRDKREKKNA ...String:
MDAMKRGLCC VLLLCGAVFV SPSQEIHARF RRGARAENLW VTVYYGVPVW KDAETTLFCA SDAKAYETEK RNVWATHCCV PTDPNPQEIH LENVTEEFNM WKNNMVEQMH EDIISLWDQS LKPCVKLTPL CVTLNCTNAT ASNSSIIEGM KNCSFNITTE LRDKREKKNA LFYKLDIVQL DGNSSQYRLI NCNTSAITQA CPKVSFEPIP IHYCAPAGFA ILKCNNKTFT GTGPCNNVST VQCTHGIKPV VSTQLLLNGS LAEGEIIIRS ENITNNVKTI LVHLNESVKI ECTRPNNKTV TSIRIGPGQW FYAYGQVIGD IREAYCNINE STWNETLGKV VKQLRKHFGN NTIIRFQPSS GGDLEVTTHS FNCGGEFFYC NTSGLFNSTW ISNTSVQGSN STGSNDSITL PCRIKQIINM WQRVGQAMYA PPIQGVIRCV SNITGLILTR DGGKNNTETF RPGGGDMRDN WRSELYKYKV VKIEPLGVAP TRCKRRVVGR RRRRRAVGIG AVSLGFLGAA GSTMGAASMT LTVQARNLLS GIVQQQSNLL RAPECQQHLL KDTHWGIKQL QARVLAVEHY LRDQQLLGIW GCSGKLICCT NVPWNSSWSN RNLSEIWDNM TWLQWDKEIS NYTQIIYGLL EESQNQQEKN EQDLLALD

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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
GridModel: Homemade / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: CONTINUOUS

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Electron microscopy

MicroscopeFEI TECNAI F20
Image recordingFilm or detector model: TVIPS TEMCAM-F416 (4k x 4k) / Detector mode: COUNTING / 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: 1.5 µm / Nominal defocus min: 1.0 µm
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: EMDB MAP
EMDB ID:

20396


Details: Low pass filtered to 40 angstroms.
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 25.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 4456
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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