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- EMDB-43917: nsEM of HIV-1 B41 SOSIP.v4.1 Env in Complex with Week 22 N611, N2... -

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Basic information

Entry
Database: EMDB / ID: EMD-43917
TitlensEM of HIV-1 B41 SOSIP.v4.1 Env in Complex with Week 22 N611, N241, Base, and Anti-Immune Complex Epitope pAbs (Rabbit ID: 1646)
Map data
Sample
  • Complex: nsEM of HIV-1 B41 SOSIP.v4.1 Env in Complex with Week 22 N611, N241, Base, and Anti-Immune Complex Epitope pAbs (Rabbit ID: 1646)
    • Complex: Rabbit Polyclonal Antibodies - N241, Base, and Anti-Immune Complex Epitope pAbs
      • Protein or peptide: HIV-1 B41 SOSIP.v4.1 - Env
    • Complex: HIV-1 B41 SOSIP.v4.1 Env
KeywordsHIV / Polyclonal / Antibodies / nsEMPEM / Rabbit / VIRAL PROTEIN
Biological speciesOryctolagus cuniculus (rabbit) / Human immunodeficiency virus 1
Methodsingle particle reconstruction / negative staining / Resolution: 22.0 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_43917.png

Downloads & links

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Map

FileDownload / File: emd_43917.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

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.77 Å
Density

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Histogram (log scale)
Contour LevelBy AUTHOR: 0.013
Minimum - Maximum-0.030666681 - 0.059220817
Average (Standard dev.)0.00008652753 (±0.0030864812)
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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Additional map: Additional Map 1 - N241, N611, Base Epitopes

Fileemd_43917_additional_1.map
AnnotationAdditional Map 1 - N241, N611, Base Epitopes
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Half map: #1

Fileemd_43917_half_map_1.map
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Half map: #2

Fileemd_43917_half_map_2.map
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Sample components

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Entire : nsEM of HIV-1 B41 SOSIP.v4.1 Env in Complex with Week 22 N611, N2...

EntireName: nsEM of HIV-1 B41 SOSIP.v4.1 Env in Complex with Week 22 N611, N241, Base, and Anti-Immune Complex Epitope pAbs (Rabbit ID: 1646)
Components
  • Complex: nsEM of HIV-1 B41 SOSIP.v4.1 Env in Complex with Week 22 N611, N241, Base, and Anti-Immune Complex Epitope pAbs (Rabbit ID: 1646)
    • Complex: Rabbit Polyclonal Antibodies - N241, Base, and Anti-Immune Complex Epitope pAbs
      • Protein or peptide: HIV-1 B41 SOSIP.v4.1 - Env
    • Complex: HIV-1 B41 SOSIP.v4.1 Env

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Supramolecule #1: nsEM of HIV-1 B41 SOSIP.v4.1 Env in Complex with Week 22 N611, N2...

SupramoleculeName: nsEM of HIV-1 B41 SOSIP.v4.1 Env in Complex with Week 22 N611, N241, Base, and Anti-Immune Complex Epitope pAbs (Rabbit ID: 1646)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 / Details: Additional Map 1 - N251, N611, Base Epitope pAbs

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Supramolecule #2: Rabbit Polyclonal Antibodies - N241, Base, and Anti-Immune Comple...

SupramoleculeName: Rabbit Polyclonal Antibodies - N241, Base, and Anti-Immune Complex Epitope pAbs
type: complex / ID: 2 / Parent: 1 / Macromolecule list: all
Source (natural)Organism: Oryctolagus cuniculus (rabbit)

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Supramolecule #3: HIV-1 B41 SOSIP.v4.1 Env

SupramoleculeName: HIV-1 B41 SOSIP.v4.1 Env / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Human immunodeficiency virus 1

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Macromolecule #1: HIV-1 B41 SOSIP.v4.1 - Env

MacromoleculeName: HIV-1 B41 SOSIP.v4.1 - Env / type: protein_or_peptide / ID: 1 / Details: The sequence contains engineered SOSIP mutations. / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MDAMKRGLCC VLLLCGAVFV SPSQEIHARF RRGARAAKKW VTVYYGVPVW KEATTTLFCA SDAKAYDTEV HNVWATHACV PTDPNPQEIV LGNVTENFNM WKNNMVEQMH EDIISLWDQS LKPCVKLTPL CVTLNCNNVN TNNTNNSTNA TISDWEKMET GEMKNCSFNV ...String:
MDAMKRGLCC VLLLCGAVFV SPSQEIHARF RRGARAAKKW VTVYYGVPVW KEATTTLFCA SDAKAYDTEV HNVWATHACV PTDPNPQEIV LGNVTENFNM WKNNMVEQMH EDIISLWDQS LKPCVKLTPL CVTLNCNNVN TNNTNNSTNA TISDWEKMET GEMKNCSFNV TTSIRDKIKK EYALFYKLDV VPLENKNNIN NTNITNYRLI NCNTSVITQA CPKVSFEPIP IHYCAPAGFA ILKCNSKTFN GSGPCTNVST VQCTHGIRPV VSTQLLLNGS LAEEEIVIRS ENITDNAKTI IVQLNEAVEI NCTRPNNNTR KSIHIGPGRA FYATGDIIGN IRQAHCNISK ARWNETLGQI VAKLEEQFPN KTIIFNHSSG GDPEIVTHSF NCGGEFFYCN TTPLFNSTWN NTRTDDYPTG GEQNITLQCR IKQIINMWQG VGKAMYAPPI RGQIRCSSNI TGLLLTRDGG RDQNGTETFR PGGGNMRDNW RSELYKYKVV KIEPLGIAPT ACKRRVAVGL GAFILGFLGA AGSTMGAASM ALTVQARLLL SGIVQQQNNL LRAPEAQQHM LQLTVWGIKQ LQARVLAVER YLRDQQLLGI WGCSGKIICC TNVPWNDSWS NKTINEIWDN MTWMQWEKEI DNYTQHIYTL LEVSQIQQEK NEQELLELD

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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 / Pretreatment - Type: PLASMA CLEANING

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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: 22.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Details: Additional Map 1 - 4162 Particles / Number images used: 3352
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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