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- EMDB-73016: Icosahedral reconstruction of EEEV at pH 5.6. -

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Basic information

Entry
Database: EMDB / ID: EMD-73016
TitleIcosahedral reconstruction of EEEV at pH 5.6.
Map data
Sample
  • Virus: Eastern equine encephalitis virus
KeywordsEastern Equine Encephalitis Virus / Cryo-EM / Single Particle Averaging / localized reconstruction / asymmetric unit / low pH back neutralization. / VIRUS
Biological speciesEastern equine encephalitis virus
Methodsingle particle reconstruction / cryo EM / Resolution: 10.4 Å
AuthorsBandyopadhyay A / Klose T / Kuhn RJ
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI095366 United States
CitationJournal: Nat Commun / Year: 2026
Title: Asymmetric structural transitions in the icosahedral organization of Eastern equine encephalitis virus.
Authors: Abhishek Bandyopadhyay / Lauren E Williamson / Cameron D Buchman / Thomas Klose / James E Crowe / Richard J Kuhn /
Abstract: Delivery of the viral genome into host cells is a critical step in successful viral infection. Alphaviruses achieve this step by fusing the viral and endosomal membranes under acidic conditions. This ...Delivery of the viral genome into host cells is a critical step in successful viral infection. Alphaviruses achieve this step by fusing the viral and endosomal membranes under acidic conditions. This process requires significant structural changes in the alphavirus glycoprotein organization. Structural characterization of acidic pH-induced conformational changes in alphavirus virions has remained elusive due to the rapid, transient nature of these states, conformational heterogeneity, and particle aggregation. Antibody binding studies conducted at elevated temperatures or under acidic pH conditions have further revealed the presence of transitional epitopes that are inaccessible on alphaviruses at room temperature or neutral pH. In this report, we present structural snapshots of the conformational changes in the glycoproteins and nucleocapsid core of a prototypical alphavirus, Eastern equine encephalitis virus, caused by exposure to 40 °C or pH 5.6. These findings provide insights into the structural transitions that occur prior to viral fusion with the endosomal membrane. This approach has also allowed us to define the molecular basis for recognition of a pan-alphavirus epitope by a patient-derived human antibody.
History
DepositionOct 3, 2025-
Header (metadata) releaseMay 27, 2026-
Map releaseMay 27, 2026-
UpdateMay 27, 2026-
Current statusMay 27, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_73016.png

Downloads & links

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Map

FileDownload / File: emd_73016.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
2.08 Å/pix.
x 512 pix.
= 1064.96 Å		2.08 Å/pix.
x 512 pix.
= 1064.96 Å		2.08 Å/pix.
x 512 pix.
= 1064.96 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 2.08 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.16235453 - 0.3100301
Average (Standard dev.)0.0017666948 (±0.044624936)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 1064.96 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_73016_half_map_1.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Half map: #2

Fileemd_73016_half_map_2.map
Projections & Slices
AxesZYX

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Sample components

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Entire : Eastern equine encephalitis virus

EntireName: Eastern equine encephalitis virus
Components
  • Virus: Eastern equine encephalitis virus

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Supramolecule #1: Eastern equine encephalitis virus

SupramoleculeName: Eastern equine encephalitis virus / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1-#3 / NCBI-ID: 11021 / Sci species name: Eastern equine encephalitis virus / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No
Host (natural)Organism: Culiseta melanura (mosquito)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration1 mg/mL
BufferpH: 5.6
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 298 K

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 36.2 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.6 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 10.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 13326
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final 3D classificationSoftware - Name: cryoSPARC

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Atomic model buiding 1

Initial modelChain - Source name: Other / Chain - Initial model type: other
RefinementProtocol: OTHER

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