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

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Open data


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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: To Be Published
Title: A single residue in the yellow fever virus envelope protein modulates virion architecture and vaccine potency
Authors: Bibby S / Jung J / Low YS / Amarilla AA / Newton ND / Scott CAP / Balk J / Ting YT / Freney ME / Liang B / Grant T / Coulibaly F / Young P / Hall R / Hobson-Peters J / Modhiran N / Watterson D
History
DepositionMar 26, 2024-
Header (metadata) releaseSep 3, 2025-
Map releaseSep 3, 2025-
UpdateSep 3, 2025-
Current statusSep 3, 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

Projections

Slices (1/2)
Density Histograms

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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