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- EMDB-43909: nsEM of HIV-1 16055 SOSIP.v8.3 Env in Complex with Week 22 N611/N... -

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Basic information

Entry
Database: EMDB / ID: EMD-43909
TitlensEM of HIV-1 16055 SOSIP.v8.3 Env in Complex with Week 22 N611/N625, V2, C3/V5 and Base Epitope pAbs (Rabbit ID: 2463)
Map data
Sample
  • Complex: nsEM of HIV-1 16055 SOSIP.v8.3 Env in Complex with Week 22 N611/N625, V2, C3/V5 and Base Epitope pAbs (Rabbit ID: 2463)
    • Complex: Rabbit Polyclonal Antibody - N611/N625, V2, C3/V5 and Base Epitopes
      • Protein or peptide: HIV-1 16055 SOSIP.v8.3 - gp140
    • Complex: HIV-1 16055 SOSIP.v8.3 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 / Antansijevic A / 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

Downloads & links

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Map

FileDownload / File: emd_43909.map.gz / Format: CCP4 / Size: 42.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
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)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.77 Å
Density
Contour LevelBy AUTHOR: 0.019
Minimum - Maximum-0.047187015 - 0.078447975
Average (Standard dev.)-0.00007501324 (±0.003880626)
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 - V2 and Base Epitopes

Fileemd_43909_additional_1.map
AnnotationAdditional Map 1 - V2 and Base Epitopes
Projections & Slices
AxesZYX

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Additional map: Additional Map 2 - C3/V5 and V2 Epitopes

Fileemd_43909_additional_2.map
AnnotationAdditional Map 2 - C3/V5 and V2 Epitopes
Projections & Slices
AxesZYX

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Half map: #2

Fileemd_43909_half_map_1.map
Projections & Slices
AxesZYX

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Density Histograms

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Half map: #1

Fileemd_43909_half_map_2.map
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Sample components

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Entire : nsEM of HIV-1 16055 SOSIP.v8.3 Env in Complex with Week 22 N611/N...

EntireName: nsEM of HIV-1 16055 SOSIP.v8.3 Env in Complex with Week 22 N611/N625, V2, C3/V5 and Base Epitope pAbs (Rabbit ID: 2463)
Components
  • Complex: nsEM of HIV-1 16055 SOSIP.v8.3 Env in Complex with Week 22 N611/N625, V2, C3/V5 and Base Epitope pAbs (Rabbit ID: 2463)
    • Complex: Rabbit Polyclonal Antibody - N611/N625, V2, C3/V5 and Base Epitopes
      • Protein or peptide: HIV-1 16055 SOSIP.v8.3 - gp140
    • Complex: HIV-1 16055 SOSIP.v8.3 Env

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Supramolecule #1: nsEM of HIV-1 16055 SOSIP.v8.3 Env in Complex with Week 22 N611/N...

SupramoleculeName: nsEM of HIV-1 16055 SOSIP.v8.3 Env in Complex with Week 22 N611/N625, V2, C3/V5 and Base Epitope pAbs (Rabbit ID: 2463)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2

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Supramolecule #2: Rabbit Polyclonal Antibody - N611/N625, V2, C3/V5 and Base Epitopes

SupramoleculeName: Rabbit Polyclonal Antibody - N611/N625, V2, C3/V5 and Base Epitopes
type: complex / ID: 2 / Parent: 1 / Macromolecule list: all
Details: Main Map - N611/N625 and V2 Epitopes Additional Map 1 - V2 and Base Epitopes Additional Map 2 - C3/V5 and V2 Epitopes
Source (natural)Organism: Oryctolagus cuniculus (rabbit)

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Supramolecule #3: HIV-1 16055 SOSIP.v8.3 Env

SupramoleculeName: HIV-1 16055 SOSIP.v8.3 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 16055 SOSIP.v8.3 - gp140

MacromoleculeName: HIV-1 16055 SOSIP.v8.3 - gp140 / 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 RRGARNGNLW VTVYYGVPVW KDAETTLFCA SDAKAYEKEK RNVWATHCCV PTDPNPQEMV LENVTENFNM WKNDMVEQMH EDVISLWDQS LKPCVKLTPL CVTLECRQVN TTNATSSVNV TNGEEIKNCS FNATTELRDK ...String:
MDAMKRGLCC VLLLCGAVFV SPSQEIHARF RRGARNGNLW VTVYYGVPVW KDAETTLFCA SDAKAYEKEK RNVWATHCCV PTDPNPQEMV LENVTENFNM WKNDMVEQMH EDVISLWDQS LKPCVKLTPL CVTLECRQVN TTNATSSVNV TNGEEIKNCS FNATTELRDK KQKVYALFYR LDIVPLEEER KGNSSKYRLI NCNTSAITQA CPKVTFDPIP IHYCAPAGYA ILKCNNKTFN GTGPCNNVST VQCTHGIKPV VSTQLLLNGS LAEGEIIIRS ENLTNNVKTI IVHLNESVEI VCTRPNNNTV KSIRIGPGQW FYYTGDIIGN IRQAYCNIKK DDWIRTLQRV GKKLAEHFPR RIINFTQPAG GDLEITTHSF NCRGEFFYCN TSSLFNSTYN PNDTNSNSSS SNSSLDITIP CRIKQIINMW QRVGQAMYAP PIEGNITCKS NITGLLLVRD GGVESNETEI FRPGGGDMRN NWRSELYKYK VVEIKPLGIA PTRCKRRVVE RRRRRRAVGL GAVSFGFLGA AGSTMGAASI TLTVQARQLL SGIVQQQSNL LKAPECQQHL LQDGHWGIKQ LQTRVLAIEH YLKDQQLLGI WGCSGKLICC TAVPWNSSWS NKSHDEIWGN MTWMQWDREI SNYTNTIYRL LEDSQNQQEQ NEKDLLALD

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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:

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: Number of particles used for the final reconstruction of Additional Map 1 (2381) and Additional Map 2 (2027).
Number images used: 2557
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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