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- EMDB-46830: Polyclonal immune complex of Fab from Rhesus Macaque BB798E at we... -

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Basic information

Entry
Database: EMDB / ID: EMD-46830
TitlePolyclonal immune complex of Fab from Rhesus Macaque BB798E at week 12 binding H1 HA
Map dataNegative stain global refinement of particle stack used to sort polyclonal responses to H1 HA from Cynomolgus Macaque BB798E at week 12
Sample
  • Complex: Polyclonal immune complex of Fab from Cynomolgus Macaque 6974 at week 12 binding H1 HA
Keywordsinfluenza / hemagglutinin / H1 / polyclonal / complex / Fab complex / viral fusion protein / VIRAL PROTEIN
Biological speciesMacaca fascicularis (crab-eating macaque)
Methodsingle particle reconstruction / negative staining / Resolution: 20.0 Å
AuthorsHan J / Rodriguez AJ / Ferguson JA / Ward AB
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)75N93019C00051 United States
CitationJournal: bioRxiv / Year: 2025
Title: Functional, Immunogenetic, and Structural Convergence in Influenza Immunity between Humans and Macaques.
Authors: Maya Sangesland / Ning Li / Yaroslav Tsybovsky / Megan D Rodgers / Julianna Han / Alesandra J Rodriguez / James A Ferguson / Amy R Henry / Sarah C Smith / Jesmine Roberts-Torres / Rebecca A ...Authors: Maya Sangesland / Ning Li / Yaroslav Tsybovsky / Megan D Rodgers / Julianna Han / Alesandra J Rodriguez / James A Ferguson / Amy R Henry / Sarah C Smith / Jesmine Roberts-Torres / Rebecca A Gillespie / Cuiping Liu / Jonah S Merriam / Tyler Stephens / Connor Williams / Emma Maestle / Martin Corcoran / Michelle Ravichandran / Adrian Creanga / Sarah F Andrews / Theodore C Pierson / Gunilla B Karlsson Hedestam / Chaim A Schramm / Douglas S Reed / Daniel C Douek / Tongqing Zhou / Andrew B Ward / Masaru Kanekiyo
Abstract: Human B cell immunity to the influenza hemagglutinin (HA) stem region, a universal influenza vaccine target, is often stereotyped and immunogenetically restricted, posing challenges for study outside ...Human B cell immunity to the influenza hemagglutinin (HA) stem region, a universal influenza vaccine target, is often stereotyped and immunogenetically restricted, posing challenges for study outside humans. Here, we show that macaques vaccinated with a HA stem immunogen elicit human-like public B cell lineages targeting two major conserved sites of vulnerability, the central stem and anchor epitopes. Central stem antibodies were predominantly derived from V 1-138, the macaque homolog of human V 1-69, a V -gene preferentially used in human central stem broadly neutralizing antibodies (bnAbs). Similarly, macaques produced anchor bnAbs with the human-like NWP motif. Both bnAb lineages were functionally and structurally analogous to their human counterparts, with recognition mediated largely by germline-encoded motifs. Thus the macaque immunoglobulin repertoire supports human-like public bnAb responses to influenza HA. Moreover, this underscores the utility of homologous germline-encoded immunity, suggesting that immune repertoires of macaques and humans may have been similarly shaped during evolution.
HIGHLIGHTS: Functional human-like public antibody lineages can be elicited to HA stem supersites in macaques. Macaque central stem bnAbs are predominantly derived from V 1-138, a V -gene homologous ...HIGHLIGHTS: Functional human-like public antibody lineages can be elicited to HA stem supersites in macaques. Macaque central stem bnAbs are predominantly derived from V 1-138, a V -gene homologous to human V 1-69. The human-like CDR L3 NWP anchor epitope-targeting lineage can be elicited in macaques.Central stem and anchor bnAbs from humans and macaques engage their respective epitopes with atomic level similarity.
History
DepositionSep 2, 2024-
Header (metadata) releaseJul 30, 2025-
Map releaseJul 30, 2025-
UpdateJul 30, 2025-
Current statusJul 30, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_46830.png

Downloads & links

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Map

FileDownload / File: emd_46830.map.gz / Format: CCP4 / Size: 34.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationNegative stain global refinement of particle stack used to sort polyclonal responses to H1 HA from Cynomolgus Macaque BB798E at week 12
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.06 Å/pix.
x 208 pix.
= 428.48 Å		2.06 Å/pix.
x 208 pix.
= 428.48 Å		2.06 Å/pix.
x 208 pix.
= 428.48 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.06 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0368
Minimum - Maximum-0.033722114 - 0.12493219
Average (Standard dev.)0.00027058515 (±0.004915929)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions208208208
Spacing208208208
CellA=B=C: 428.47998 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Negative stain map of polyclonal Fab binding the...

Fileemd_46830_additional_1.map
AnnotationNegative stain map of polyclonal Fab binding the H1 HA central stem 1 epitope from Rhesus Macaque BB798E at week 12
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Additional map: Negative stain map of polyclonal Fab binding the...

Fileemd_46830_additional_2.map
AnnotationNegative stain map of polyclonal Fab binding the H1 HA anchor epitope from Rhesus Macaque BB798E at week 12
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Negative stain map of polyclonal Fab binding the...

Fileemd_46830_additional_3.map
AnnotationNegative stain map of polyclonal Fab binding the H1 HA central stem 2 epitope from Rhesus Macaque BB798E at week 12
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Negative stain map of polyclonal Fab binding the...

Fileemd_46830_additional_4.map
AnnotationNegative stain map of polyclonal Fab binding the H1 HA central stem 3 epitope from Rhesus Macaque BB798E at week 12
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Negative stain map of polyclonal Fab binding the...

Fileemd_46830_additional_5.map
AnnotationNegative stain map of polyclonal Fab binding the H1 HA low stem epitope from Rhesus Macaque BB798E at week 12
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Negative stain half map A for global refinement...

Fileemd_46830_half_map_1.map
AnnotationNegative stain half map A for global refinement of particle stack used to sort polyclonal responses to H1 HA from Rhesus Macaque BB798E at week 12
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Negative stain half map B for global refinement...

Fileemd_46830_half_map_2.map
AnnotationNegative stain half map B for global refinement of particle stack used to sort polyclonal responses to H1 HA from Cynomolgus Macaque BB798E at week 12
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 immune complex of Fab from Cynomolgus Macaque 6974 at ...

EntireName: Polyclonal immune complex of Fab from Cynomolgus Macaque 6974 at week 12 binding H1 HA
Components
  • Complex: Polyclonal immune complex of Fab from Cynomolgus Macaque 6974 at week 12 binding H1 HA

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Supramolecule #1: Polyclonal immune complex of Fab from Cynomolgus Macaque 6974 at ...

SupramoleculeName: Polyclonal immune complex of Fab from Cynomolgus Macaque 6974 at week 12 binding H1 HA
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Macaca fascicularis (crab-eating macaque)
Molecular weightTheoretical: 280 KDa

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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

Concentration0.015 mg/mL
BufferpH: 7.4
StainingType: NEGATIVE / Material: 2% w/v uranyl formate
GridModel: Homemade / Material: COPPER / Mesh: 400 / Support film - Material: CARBON

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Electron microscopy

MicroscopeFEI TECNAI SPIRIT
Image recordingFilm or detector model: FEI EAGLE (4k x 4k) / Average electron dose: 25.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: LAB6
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: DARK FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.5 µm
Sample stageSpecimen holder model: SIDE ENTRY, EUCENTRIC / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Tecnai Spirit / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

4m4y

Final reconstructionResolution.type: BY AUTHOR / Resolution: 20.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 20514
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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