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- EMDB-56922: Polyclonal immune complex comprising AMC009 SOSIP.v4.2 in complex... -

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Basic information

Entry
Database: EMDB / ID: EMD-56922
TitlePolyclonal immune complex comprising AMC009 SOSIP.v4.2 in complex with polyclonal antibodies from rabbit UA0065 - Obtained by negative stain EM.
Map dataMain map generated by 3D refinement of the particle subset corresponding to the AMC009 SOSIP.v4.2 antigen complexed with polyclonal antibodies from rabbit UA0065
Sample
  • Complex: Polyclonal antibody from rabbit UA0065 in complex with AMC009 SOSIP.v4.2
    • Protein or peptide: AMC009 SOSIP.v4.2
KeywordsAntigen / antibody / complex / HIV / VIRAL PROTEIN
Biological speciesHuman immunodeficiency virus 1
Methodsingle particle reconstruction / negative staining / Resolution: 20.0 Å
AuthorsBrown S / Eray ER / Antanasijevic A
Funding support United States, 2 items
OrganizationGrant numberCountry
amfAR110413-73-RKVA United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI36621 United States
CitationJournal: bioRxiv / Year: 2026
Title: Decoding epitope immunodominance in HIV Env using cryoEM and machine learning.
Authors: Jan S Schuhmacher / Shuhao Xiao / Elise R Eray / Sharidan Brown / Alexander Zambrowski / Aryan Jain / Daniel Montiel Garcia / Gabriel Ozorowski / Wenwen Zhu / Katrina Saam / Tom G Caniels / ...Authors: Jan S Schuhmacher / Shuhao Xiao / Elise R Eray / Sharidan Brown / Alexander Zambrowski / Aryan Jain / Daniel Montiel Garcia / Gabriel Ozorowski / Wenwen Zhu / Katrina Saam / Tom G Caniels / John P Moore / Max Crispin / Rogier W Sanders / Srirupa Chakraborty / Bruno E Correia / Andrew B Ward / Aleksandar Antanasijevic /
Abstract: Viral surface glycoproteins, such as the HIV envelope protein (Env), present numerous antibody (Ab) epitopes, yet immune responses consistently focus on only a subset, a phenomenon known as ...Viral surface glycoproteins, such as the HIV envelope protein (Env), present numerous antibody (Ab) epitopes, yet immune responses consistently focus on only a subset, a phenomenon known as immunodominance. Although structural studies have provided insights into Env antigenicity, our understanding of the molecular features that govern efficient Ab engagement remains incomplete, thereby limiting the predictive and rational design of vaccines. Here, we characterized the structural determinants of epitope immunodominance in HIV Env by integrating high-resolution cryoEM-based polyclonal epitope mapping (cryoEMPEM) across different clades with quantitative analyses of epitope topology, accessibility, and physicochemical properties. More than 70 new structures were resolved to assemble a library of >100 Env-antibody complexes. These data informed the development of a surface-centric, machine-learning model to predict relative ntigen urface mmunodominance (ASI model). Comparison of ASI-predicted epitope sites with the specificities of Env-induced antibodies showed that the model accurately identifies immunodominant regions and highlights the structural features driving immune bias. Notably, immunogens redesigned based on model predictions successfully redirected Ab responses toward a normally subdominant epitope, demonstrating the potential of strategies coupling targeted assembly of focused structural libraries with machine learning to uncover complex molecular patterns and enable design of more effective vaccine antigens.
History
DepositionFeb 25, 2026-
Header (metadata) releaseApr 22, 2026-
Map releaseApr 22, 2026-
UpdateApr 22, 2026-
Current statusApr 22, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_56922.png

Downloads & links

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Map

FileDownload / File: emd_56922.map.gz / Format: CCP4 / Size: 42.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMain map generated by 3D refinement of the particle subset corresponding to the AMC009 SOSIP.v4.2 antigen complexed with polyclonal antibodies from rabbit UA0065
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

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.015
Minimum - Maximum-0.024679039 - 0.04800779
Average (Standard dev.)0.00022215894 (±0.0030843078)
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: Half map 1 generated by 3D refinement of...

Fileemd_56922_half_map_1.map
AnnotationHalf map 1 generated by 3D refinement of the particle subset corresponding to the AMC009 SOSIP.v4.2 antigen complexed with polyclonal antibodies from rabbit UA0065
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 2 generated by 3D refinement of...

Fileemd_56922_half_map_2.map
AnnotationHalf map 2 generated by 3D refinement of the particle subset corresponding to the AMC009 SOSIP.v4.2 antigen complexed with polyclonal antibodies from rabbit UA0065
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Polyclonal antibody from rabbit UA0065 in complex with AMC009 SOS...

EntireName: Polyclonal antibody from rabbit UA0065 in complex with AMC009 SOSIP.v4.2
Components
  • Complex: Polyclonal antibody from rabbit UA0065 in complex with AMC009 SOSIP.v4.2
    • Protein or peptide: AMC009 SOSIP.v4.2

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Supramolecule #1: Polyclonal antibody from rabbit UA0065 in complex with AMC009 SOS...

SupramoleculeName: Polyclonal antibody from rabbit UA0065 in complex with AMC009 SOSIP.v4.2
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: Antigen was recombinantly expressed while the antibodies were obtained from a natural source (rabbit).
Source (natural)Organism: Human immunodeficiency virus 1

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Macromolecule #1: AMC009 SOSIP.v4.2

MacromoleculeName: AMC009 SOSIP.v4.2 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MDAMKRGLCC VLLLCGAVFV SPSQEIHARF RRGARADKLW VTVYYGVPVW KEATTTLFCA SDAKAYDTEV RNVWATHACV PTDPNPQEVV LENVTENFNM WKNDMVEQMH EDIISLWDQS LKPCVKLTPL CVTLNCTDYV GNATNASTTN ATGGIGGTVE RGEIKNCSFN ...String:
MDAMKRGLCC VLLLCGAVFV SPSQEIHARF RRGARADKLW VTVYYGVPVW KEATTTLFCA SDAKAYDTEV RNVWATHACV PTDPNPQEVV LENVTENFNM WKNDMVEQMH EDIISLWDQS LKPCVKLTPL CVTLNCTDYV GNATNASTTN ATGGIGGTVE RGEIKNCSFN ITTSIRDKVQ KEYALFYKLD IVPIDNDNTN NSYRLINCNT SVIKQACPKV SFEPIPIHYC APAGFAILKC NDKKFNGTGP CTNVSTVQCT HGIRPVVSTQ LLLNGSLAEK EVVIRSQNFT NNAKVIIVQL NESVVINCTR PNNNTRKSIH IAPGRWFYTT GAIIGDIRQA HCNISRVKWN NTLKQIATKL REQFKNKTIA FNQSSGGDPE IVMHSFNCGG EFFYCNTTQL FNSTWNDTEV SNYNDITHIT LPCRIKQIIN MWQKVGKAMY APPIRGQIRC SSNITGLLLT RDGGSNENKT SETETFRPAG GDMRDNWRSE LYKYKVVKIE PLGVAPTKCK RRVVQRRRRR RAVGAIGAVF LGFLGAAGST MGAASMTLTV QARQLLSGIV QQQNNLLRAP EAQQHMLKLT VWGIKQLQAR VLAVERYLRD QQLLGIWGCS GKLICCTAVP WNNSWSNRSL DMIWNNMTWI EWEREIDNYT GLIYNLLEES QNQQEKNEQE LLELD

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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

Concentration0.05 mg/mL
BufferpH: 7.4
Component:
ConcentrationFormulaName
20.0 mMTrisTris
150.0 mMNaClSalt

Details: TBS
StainingType: NEGATIVE / Material: UF 2%
GridModel: Homemade / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR

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Electron microscopy

MicroscopeFEI TECNAI F20
Image recordingFilm or detector model: TVIPS TEMCAM-F416 (4k x 4k) / Number grids imaged: 1 / 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: 20.0 µm / Nominal defocus min: 15.0 µm / Nominal magnification: 62000
Sample stageSpecimen holder model: SIDE ENTRY, EUCENTRIC / Cooling 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: OTHER / Details: Low pass filtered map of the HIV-ENV ectodomain
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 20.0 Å / Resolution method: OTHER / Software - Name: RELION (ver. 3) / Details: Low-pass filter / Number images used: 4806
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3)
Final 3D classificationNumber classes: 50 / Software - Name: RELION (ver. 3)

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