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- EMDB-56927: Polyclonal immune complex comprising B41 SOSIP.v4.1 in complex wi... -

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Basic information

Entry
Database: EMDB / ID: EMD-56927
TitlePolyclonal immune complex comprising B41 SOSIP.v4.1 in complex with polyclonal antibodies from rabbit r1645 - Obtained by negative stain EM.
Map dataMain map generated by 3D refinement of the particle subset corresponding to the B41 SOSIP.v4.1 antigen complexed with polyclonal antibodies from rabbit r1645
Sample
  • Complex: Polyclonal antibody from rabbit r1645 in complex with B41 SOSIP.v4.1
    • Protein or peptide: B41 SOSIP.v4.1
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
Other private110413-73-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_56927.png

Downloads & links

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Map

FileDownload / File: emd_56927.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 B41 SOSIP.v4.1 antigen complexed with polyclonal antibodies from rabbit r1645
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: 0.01
Minimum - Maximum-0.02298971 - 0.0546057
Average (Standard dev.)0.00018983116 (±0.0031244818)
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 generated by 3D refinement of the...

Fileemd_56927_additional_1.map
AnnotationAdditional map generated by 3D refinement of the particle subset corresponding to the B41 SOSIP.v4.1 antigen complexed with polyclonal antibodies from rabbit r1645
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_56927_half_map_1.map
AnnotationHalf map 2 generated by 3D refinement of the particle subset corresponding to the B41 SOSIP.v4.1 antigen complexed with polyclonal antibodies from rabbit r1645
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 1 generated by 3D refinement of...

Fileemd_56927_half_map_2.map
AnnotationHalf map 1 generated by 3D refinement of the particle subset corresponding to the B41 SOSIP.v4.1 antigen complexed with polyclonal antibodies from rabbit r1645
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 r1645 in complex with B41 SOSIP.v4.1

EntireName: Polyclonal antibody from rabbit r1645 in complex with B41 SOSIP.v4.1
Components
  • Complex: Polyclonal antibody from rabbit r1645 in complex with B41 SOSIP.v4.1
    • Protein or peptide: B41 SOSIP.v4.1

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Supramolecule #1: Polyclonal antibody from rabbit r1645 in complex with B41 SOSIP.v4.1

SupramoleculeName: Polyclonal antibody from rabbit r1645 in complex with B41 SOSIP.v4.1
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: B41 SOSIP.v4.1

MacromoleculeName: B41 SOSIP.v4.1 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MDAMKRGLCC VLLLCGAVFV SPSQEIHARF RRGARAAKKW VTVYYGVPVW KEATTTLFCA SDAKAYDTKV HNVWATHACV PTDPNPQEIV LGNVTENFNM WKNNMVEQMH EDIISLWDQS LKPCVKLTPL CVTLNCNNVN TNNTNNSTNA TISDWEKMET GEMKNCSFNV ...String:
MDAMKRGLCC VLLLCGAVFV SPSQEIHARF RRGARAAKKW VTVYYGVPVW KEATTTLFCA SDAKAYDTKV 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 KSIHIGPGRW FYATGDIIGN IRQAHCNISK ARWNETLGQI VAKLEEQFPN KTIIFNHSSG GDPEIVTHSF NCGGEFFYCN TTPLFNSTWN NTRTDDYPTG GEQNITLQCR IKQIINMWQG VGKAMYAPPI RGQIRCSSNI TGLLLTRDGG RDQNGTETFR PGGGNMRDNW RSELYKYKVV KIEPLGIAPT ACKRRVVQRR RRRRAVGLGA FILGFLGAAG STMGAASMAL TVQARNLLSG IVQQQNNLLR APEAQQHMLQ LTVWGIKQLQ ARVLAVERYL RDQQLLGIWG CSGKIICCTN VPWNDSWSNK TINEIWDNMT WMQWEKEIDN YTQHIYTLLE VSQIQQEKNE QELLELD

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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: 5496
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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