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- EMDB-44076: nsEM of HIV-1 BG505 SOSIP.v5.2 (N289/N241) Env in Complex with We... -

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Basic information

Entry
Database: EMDB / ID: EMD-44076
TitlensEM of HIV-1 BG505 SOSIP.v5.2 (N289/N241) Env in Complex with Week 38 gp120-Interface, N289, C3/V5, Base, and Anti-Immune Complex Epitope pAbs (NHP ID: Rh33203)
Map data
Sample
  • Complex: Macaque Polyclonal Antibodies - gp120-Interface, N289, C3/V5, Base, and Anti-Immune Complex Epitope pAbs
    • Complex: HIV-1 BG505 SOSIP.v5.2 (N289/N241) Env
      • Protein or peptide: HIV-1 BG505 SOSIP.v5.2 (N289/N241) Env - gp140
KeywordsHIV / Polyclonal / Antibodies / nsEMPEM / Macaque / VIRAL PROTEIN
Biological speciesMacaca mulatta (Rhesus monkey) / Human immunodeficiency virus 1
Methodsingle particle reconstruction / negative staining / Resolution: 25.0 Å
AuthorsBrown S / Sewall LM / Ward AB
Funding support United States, 3 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
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)UM1 AI100663 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 13, 2024-
Header (metadata) releaseJan 29, 2025-
Map releaseJan 29, 2025-
UpdateJan 29, 2025-
Current statusJan 29, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_44076.png

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Map

FileDownload / File: emd_44076.map.gz / Format: CCP4 / Size: 42.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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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

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.98 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.005
Minimum - Maximum-0.04463391 - 0.104150385
Average (Standard dev.)0.00006959643 (±0.0044871657)
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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Additional map: Additional Map 1 - gp120-Interface, C3/V5, N289, Base Epitopes

Fileemd_44076_additional_1.map
AnnotationAdditional Map 1 - gp120-Interface, C3/V5, N289, Base Epitopes
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Half map: #1

Fileemd_44076_half_map_1.map
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Half map: #2

Fileemd_44076_half_map_2.map
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Sample components

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Entire : Macaque Polyclonal Antibodies - gp120-Interface, N289, C3/V5, Bas...

EntireName: Macaque Polyclonal Antibodies - gp120-Interface, N289, C3/V5, Base, and Anti-Immune Complex Epitope pAbs
Components
  • Complex: Macaque Polyclonal Antibodies - gp120-Interface, N289, C3/V5, Base, and Anti-Immune Complex Epitope pAbs
    • Complex: HIV-1 BG505 SOSIP.v5.2 (N289/N241) Env
      • Protein or peptide: HIV-1 BG505 SOSIP.v5.2 (N289/N241) Env - gp140

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Supramolecule #1: Macaque Polyclonal Antibodies - gp120-Interface, N289, C3/V5, Bas...

SupramoleculeName: Macaque Polyclonal Antibodies - gp120-Interface, N289, C3/V5, Base, and Anti-Immune Complex Epitope pAbs
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Macaca mulatta (Rhesus monkey)

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Supramolecule #2: HIV-1 BG505 SOSIP.v5.2 (N289/N241) Env

SupramoleculeName: HIV-1 BG505 SOSIP.v5.2 (N289/N241) Env / type: complex / ID: 2 / Parent: 1 / Macromolecule list: all
Source (natural)Organism: Human immunodeficiency virus 1

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Macromolecule #1: HIV-1 BG505 SOSIP.v5.2 (N289/N241) Env - gp140

MacromoleculeName: HIV-1 BG505 SOSIP.v5.2 (N289/N241) Env - gp140 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
SequenceString: MDAMKRGLCC VLLLCGAVFV SPSQEIHARF RRGARAENLW VTVYYGVPVW KDAETTLFCA SDAKAYETKK HNVWATHCCV PTDPNPQEIH LENVTEEFNM WKNNMVEQMH TDIISLWDQS LKPCVKLTPL CVTLQCTNVT NNITDDMRGE LKNCSFNMTT ELRDKKQKVY ...String:
MDAMKRGLCC VLLLCGAVFV SPSQEIHARF RRGARAENLW VTVYYGVPVW KDAETTLFCA SDAKAYETKK HNVWATHCCV PTDPNPQEIH LENVTEEFNM WKNNMVEQMH TDIISLWDQS LKPCVKLTPL CVTLQCTNVT NNITDDMRGE LKNCSFNMTT ELRDKKQKVY SLFYRLDVVQ INENQGNRSN NSNKEYRLIN CNTSAITQAC PKVSFEPIPI HYCAPAGFAI LKCKDKKFNG TGPCTNVSTV QCTHGIKPVV STQLLLNGSL AEEEVIIRSE NITNNAKNIL VQLNESVQIN CTRPNNNTRK SIRIGPGQWF YATGDIIGDI RQAHCNVSKA TWNETLGKVV KQLRKHFGNN TIIRFANSSG GDLEVTTHSF NCGGEFFYCN TSGLFNSTWI SNTSVQGSNS TGSNDSITLP CRIKQIINMW QRIGQAMYAP PIQGVIRCVS NITGLILTRD GGSTNSTTET FRPGGGDMRD NWRSELYKYK VVKIEPLGVA PTRCKRRVVG RRRRRRAVGI GAVFLGFLGA AGSTMGAASM TLTVQARNLL SGIVQQQSNL LRAPECQQHL LKLTVWGIKQ LQARVLAVER YLRDQQLLGI WGCSGKLICC TNVPWNSTWS NRNLSEIWDN MTWLQWDKEI SNYTQIIYGL LEESQNQQEK NEQDLLALD

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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 TALOS ARCTICA
Image recordingFilm or detector model: FEI CETA (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: Talos Arctica / Image courtesy: FEI Company

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Image processing

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) / Details: Additional Map 1 - 3120 Particles / Number images used: 3934
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final 3D classificationNumber classes: 20 / Software - Name: RELION (ver. 3.0)

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