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- EMDB-70151: Salamander influenza-like virus (SILV) HA -

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Basic information

Entry
Database: EMDB / ID: EMD-70151
TitleSalamander influenza-like virus (SILV) HA
Map data
Sample
  • Complex: Salamander influenza-like virus (SILV) HA trimer
KeywordsSalamander influenza-like virus / SILV / Hemagglutinin / HA / VIRUS
Biological speciesSalamander influenza-like virus
Methodsingle particle reconstruction / negative staining / Resolution: 25.0 Å
AuthorsHuang J / Han J / Ward AB
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)75N93019C00051 United States
CitationJournal: bioRxiv / Year: 2025
Title: Characterization of the glycoproteins of novel fish influenza B-like viruses.
Authors: Gagandeep Singh / Jiachen Huang / Disha Bhavsar / Kirill Vasilev / James A Ferguson / Geert-Jan Boons / Viviana Simon / Robert P de Vries / Julianna Han / Andrew Ward / Florian Krammer /
Abstract: Novel influenza-like virus sequences previously identified in fish and amphibians were found to cluster as a sister clade of influenza B viruses, but have thus far remained uncharacterized. We ...Novel influenza-like virus sequences previously identified in fish and amphibians were found to cluster as a sister clade of influenza B viruses, but have thus far remained uncharacterized. We demonstrate that salamander influenza-like virus (SILV) HA is functionally divergent from influenza B virus HA and does not bind to α 2,3- and α2,6-linked sialic acids. However, the HAs of Siamese algae-eater influenza-like virus (SAEILV) and chum salmon influenza-like virus (CSILV) bind to α2,3 linked sialic acid. Furthermore, SAEILV HA binds to sialyated Lewis X, is activated by human airway enzymes and is fusogenic at a wide range of pH conditions. SAEILV NA has a highly conserved active site and a similar structure to other known NAs. We also determined the cryo-electron microscopy structure of the HA of a previously described virus from the same sister clade, the Wuhan spiny eel influenza virus (WSEIV). Importantly, no cross-reactive antibodies against these HAs or NAs were found in the human serum, suggesting that humans are immunologically naïve to these viruses.
History
DepositionApr 10, 2025-
Header (metadata) releaseAug 6, 2025-
Map releaseAug 6, 2025-
UpdateAug 6, 2025-
Current statusAug 6, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_70151.png

Downloads & links

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Map

FileDownload / File: emd_70151.map.gz / Format: CCP4 / Size: 22.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.06 Å/pix.
x 180 pix.
= 371.34 Å		2.06 Å/pix.
x 180 pix.
= 371.34 Å		2.06 Å/pix.
x 180 pix.
= 371.34 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.063 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.25
Minimum - Maximum-0.38618875 - 2.3671603
Average (Standard dev.)0.0013400008 (±0.07598133)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions180180180
Spacing180180180
CellA=B=C: 371.34 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_70151_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_70151_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 : Salamander influenza-like virus (SILV) HA trimer

EntireName: Salamander influenza-like virus (SILV) HA trimer
Components
  • Complex: Salamander influenza-like virus (SILV) HA trimer

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Supramolecule #1: Salamander influenza-like virus (SILV) HA trimer

SupramoleculeName: Salamander influenza-like virus (SILV) HA trimer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Salamander influenza-like virus

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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

Concentration0.01 mg/mL
BufferpH: 7.4
Component:
ConcentrationFormulaName
50.0 mMTrisTris
150.0 mMNaClSodium chloride
StainingType: NEGATIVE / Material: Uranyl formate
GridModel: Homemade / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE

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Electron microscopy

MicroscopeFEI TECNAI SPIRIT
Image recordingFilm or detector model: FEI EAGLE (4k x 4k) / Average electron dose: 25.0 e/Å2
Electron beamAcceleration voltage: 120 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.5 µm / Nominal defocus min: 1.0 µm
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Tecnai Spirit / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: INSILICO MODEL / Details: CryoSPARC Ab-initio
Final reconstructionResolution.type: BY AUTHOR / Resolution: 25.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: cryoSPARC (ver. 4.0) / Number images used: 19579
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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