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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: Zheng C / Rubio AA / Vasquez S / Pham D / Pan Z / Barnes CO / Kim PS
History
DepositionAug 27, 2025-
Header (metadata) releaseJan 21, 2026-
Map releaseJan 21, 2026-
UpdateJan 21, 2026-
Current statusJan 21, 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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