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- EMDB-72372: Polyclonal immune complex of guinea pig Fab from sera binding Ebo... -

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Basic information

Entry
Database: EMDB / ID: EMD-72372
TitlePolyclonal immune complex of guinea pig Fab from sera binding Ebola glycoprotein (nsEM, GP-trimer map 4)
Map dataMap derived from Relion, a low pass of 15A applied.
Sample
  • Complex: Ebola GP bound by guinea pig Fab from sera
    • Complex: Ebola GP
    • Complex: guinea pig Fab
KeywordsEbola / EBOV / Fab / nsEMPEM / ANTIVIRAL PROTEIN
Biological speciesEbola virus - Mayinga, Zaire, 1976 / Cavia porcellus (domestic guinea pig)
Methodsingle particle reconstruction / negative staining / Resolution: 15.0 Å
AuthorsRubio AA / Vasquez S / Barnes CO
Funding support United States, 1 items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: ACS Cent Sci / Year: 2026
Title: Oriented Multivalent Display Drives Consistent Serum Immunodominance to the Ebola Virus Glycoprotein.
Authors: Chu Zheng / Adonis A Rubio / Sheena Vasquez / Dominic Pham / Zhuangyu Pan / Christopher O Barnes / Peter S Kim /
Abstract: Despite the vast diversity of B cell repertoires, serum antibody responses during viral infection often focus on a limited set of epitopesa phenomenon known as immunodominance. This inherent bias ...Despite the vast diversity of B cell repertoires, serum antibody responses during viral infection often focus on a limited set of epitopesa phenomenon known as immunodominance. This inherent bias establishes a hierarchy of epitope responses, which often facilitates viral immune evasion and presents a major challenge for universal vaccine design. It remains unclear whether serum immunodominance is primarily driven by antigen-intrinsic properties or by the spatial constraints imposed by virion-bound antigen presentation. Here, using Ebola virus glycoprotein (GP) as a model system, we found that trimeric GP elicited varied epitope hierarchies between individual animals during primary immunization. In contrast, multivalent GP presentation on either a vesicular stomatitis virus or ferritin nanoparticlesin the native orientation found on the Ebola viruselicited highly consistent and more refined epitope hierarchies across multiple mice and guinea pigs. These findings reveal a key role of oriented multivalent presentation in shaping serum immunodominance. The striking consistency of epitope hierarchy among individuals suggests that oriented multivalent presentation may promote more uniform immune protection at the population level, beyond increasing the magnitude of antibody binding and neutralizing responses.
History
DepositionAug 27, 2025-
Header (metadata) releaseJan 21, 2026-
Map releaseJan 21, 2026-
UpdateApr 1, 2026-
Current statusApr 1, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_72372.png

Downloads & links

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Map

FileDownload / File: emd_72372.map.gz / Format: CCP4 / Size: 8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMap derived from Relion, a low pass of 15A applied.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.5 Å/pix.
x 128 pix.
= 320. Å		2.5 Å/pix.
x 128 pix.
= 320. Å		2.5 Å/pix.
x 128 pix.
= 320. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.5 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0676
Minimum - Maximum-0.041206762 - 0.14788054
Average (Standard dev.)0.0011462016 (±0.0127664795)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions128128128
Spacing128128128
CellA=B=C: 320.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Map derived directly from Relion from experimental data.

Fileemd_72372_additional_1.map
AnnotationMap derived directly from Relion from experimental data.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map 2

Fileemd_72372_half_map_1.map
Annotationhalf map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map 1

Fileemd_72372_half_map_2.map
Annotationhalf map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Ebola GP bound by guinea pig Fab from sera

EntireName: Ebola GP bound by guinea pig Fab from sera
Components
  • Complex: Ebola GP bound by guinea pig Fab from sera
    • Complex: Ebola GP
    • Complex: guinea pig Fab

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Supramolecule #1: Ebola GP bound by guinea pig Fab from sera

SupramoleculeName: Ebola GP bound by guinea pig Fab from sera / type: complex / ID: 1 / Parent: 0
Details: Ebola Zaire glycoprotein (GP) bound by Fab isolated from guinea pig sera at week 7 following immunization by soluble trimeric GP

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Supramolecule #2: Ebola GP

SupramoleculeName: Ebola GP / type: complex / ID: 2 / Parent: 1
Source (natural)Organism: Ebola virus - Mayinga, Zaire, 1976

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Supramolecule #3: guinea pig Fab

SupramoleculeName: guinea pig Fab / type: complex / ID: 3 / Parent: 1
Source (natural)Organism: Cavia porcellus (domestic guinea pig)

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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

Concentration0.012 mg/mL
BufferpH: 8
Component:
ConcentrationNameFormula
20.0 mMTris-Hydrochloride
150.0 mMSodium ChlorideNaCl
StainingType: NEGATIVE / Material: uranyl formate
GridModel: EMS Lacey Carbon / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: LACEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec.

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number grids imaged: 1 / Number real images: 901 / Average exposure time: 13.9 sec. / Average electron dose: 20.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.5 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 57000
Sample stageCooling holder cryogen: NITROGEN

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Image processing

Particle selectionNumber selected: 30566415
CTF correctionSoftware - Name: RELION / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

5kel


Details: PDB 5KEL with a mol map of 5 angstrom applied
Final reconstructionResolution.type: BY AUTHOR / Resolution: 15.0 Å / Resolution method: OTHER / Software - Name: RELION
Details: Low pass filter applied for final map to 15 angstroms
Number images used: 139445
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final 3D classificationSoftware - Name: RELION

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