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- EMDB-44280: Chimeric flavivirus between BinJV and YFV-17D in complex with 2C9 Fab -

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Basic information

Entry
Database: EMDB / ID: EMD-44280
TitleChimeric flavivirus between BinJV and YFV-17D in complex with 2C9 Fab
Map data
Sample
  • Complex: Yellow fever virus
    • Complex: 2C9 Fab
    • Virus: Yellow fever virus
KeywordsFlavivirus / Envelope protein / Yellow fever virus / Chimera / VIRUS
Biological speciesMus musculus (house mouse) / Yellow fever virus
Methodsingle particle reconstruction / cryo EM / Resolution: 7.3 Å
AuthorsBibby S / Jung J / Modhiran N / Watterson D
Funding support Australia, 2 items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)APP1164216 Australia
National Health and Medical Research Council (NHMRC, Australia)APP2004582 Australia
CitationJournal: Nat Commun / Year: 2025
Title: A single residue in the yellow fever virus envelope protein modulates virion architecture and antigenicity.
Authors: Summa Bibby / James Jung / Yu Shang Low / Alberto A Amarilla / Natalee D Newton / Connor A P Scott / Jessica Balk / Yi Tian Ting / Morgan E Freney / Benjamin Liang / Timothy Grant / Fasséli ...Authors: Summa Bibby / James Jung / Yu Shang Low / Alberto A Amarilla / Natalee D Newton / Connor A P Scott / Jessica Balk / Yi Tian Ting / Morgan E Freney / Benjamin Liang / Timothy Grant / Fasséli Coulibaly / Paul Young / Roy A Hall / Jody Hobson-Peters / Naphak Modhiran / Daniel Watterson /
Abstract: Yellow fever virus (YFV) is a re-emerging flavivirus that causes severe hepatic disease and mortality in humans. Despite being researched for over a century, the structure of YFV has remained elusive. ...Yellow fever virus (YFV) is a re-emerging flavivirus that causes severe hepatic disease and mortality in humans. Despite being researched for over a century, the structure of YFV has remained elusive. Here we use a chimeric virus platform to resolve the first high resolution cryo-EM structures of YFV. Stark differences in particle morphology and homogeneity are observed between vaccine and virulent strains of YFV, and these are found to have significant implications on antibody recognition and neutralisation. We identify a single residue (R380) in the YFV envelope protein that stabilises the virion surface, and leads to reduced exposure of the cross-reactive fusion loop epitope. The differences in virion morphology between YFV strains also contribute to the reduced sensitivity of the virulent YFV virions to vaccine-induced antibodies. These findings have significant implications for YFV biology, vaccinology and structure-based flavivirus antigen design.
History
DepositionMar 26, 2024-
Header (metadata) releaseSep 3, 2025-
Map releaseSep 3, 2025-
UpdateOct 8, 2025-
Current statusOct 8, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_44280.png

Downloads & links

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Map

FileDownload / File: emd_44280.map.gz / Format: CCP4 / Size: 1.6 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.96 Å/pix.
x 750 pix.
= 720. Å		0.96 Å/pix.
x 750 pix.
= 720. Å		0.96 Å/pix.
x 750 pix.
= 720. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.96 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.007
Minimum - Maximum-0.0038362278 - 0.018616667
Average (Standard dev.)0.0012240859 (±0.0022018605)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions750750750
Spacing750750750
CellA=B=C: 720.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_44280_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_44280_half_map_2.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Sample components

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Entire : Yellow fever virus

EntireName: Yellow fever virus
Components
  • Complex: Yellow fever virus
    • Complex: 2C9 Fab
    • Virus: Yellow fever virus

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Supramolecule #1: Yellow fever virus

SupramoleculeName: Yellow fever virus / type: complex / ID: 1 / Parent: 0
Details: YFV envelope and membrane proteins expressed in the backbone of Binjari virus

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Supramolecule #3: 2C9 Fab

SupramoleculeName: 2C9 Fab / type: complex / ID: 3 / Parent: 1
Source (natural)Organism: Mus musculus (house mouse)

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Supramolecule #2: Yellow fever virus

SupramoleculeName: Yellow fever virus / type: virus / ID: 2 / Parent: 1 / NCBI-ID: 11089 / Sci species name: Yellow fever virus / Virus type: VIRION / Virus isolate: OTHER / Virus enveloped: Yes / Virus empty: No

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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

BufferpH: 8
Component:
ConcentrationFormulaName
120.0 nMNaClSodium chloride
10.0 mMNH2C(CH2OH)3Tris-base
1.0 mMC10H16N2O8EDTA
VitrificationCryogen name: ETHANE / Instrument: LEICA EM GP

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Electron microscopy

MicroscopeJEOL CRYO ARM 300
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 54.25 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 20.0 µm / Nominal defocus min: 20.0 µm

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Image processing

CTF correctionSoftware - Name: CTFFIND (ver. 4) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Details: Reconstruction of a mature flavivirus (generated in-house) and low-pass filtered
Final reconstructionResolution.type: BY AUTHOR / Resolution: 7.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1.3) / Number images used: 1751
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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