[English] 日本語
Yorodumi
- EMDB-70148: CryoEM structure of Siamese algae-eater influenza-like virus (SAE... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-70148
TitleCryoEM structure of Siamese algae-eater influenza-like virus (SAEILV) NA
Map data
Sample
  • Complex: Siamese algae-eater influenza-like virus (SAEILV) NA tetramer
    • Protein or peptide: Neuraminidase
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsSiamese algae-eater influenza-like virus / SAEILV / Flu neuraminidase / NA / VIRUS / HYDROLASE
Function / homology
Function and homology information


exo-alpha-sialidase / exo-alpha-sialidase activity / carbohydrate metabolic process / host cell plasma membrane / virion membrane / metal ion binding / membrane
Similarity search - Function
Glycoside hydrolase, family 34 / Neuraminidase / Sialidase superfamily
Similarity search - Domain/homology
Biological speciesSiamese algae-eater influenza-like virus
Methodsingle particle reconstruction / cryo EM / Resolution: 2.75 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

-
Structure visualization

Supplemental images

emd_70148.png

Downloads & links

-
Map

FileDownload / File: emd_70148.map.gz / Format: CCP4 / Size: 274.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.72 Å/pix.
x 416 pix.
= 298.688 Å		0.72 Å/pix.
x 416 pix.
= 298.688 Å		0.72 Å/pix.
x 416 pix.
= 298.688 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.718 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-0.88360834 - 1.1459613
Average (Standard dev.)0.000024707255 (±0.0269213)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions416416416
Spacing416416416
CellA=B=C: 298.688 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_70148_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_70148_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_70148_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Siamese algae-eater influenza-like virus (SAEILV) NA tetramer

EntireName: Siamese algae-eater influenza-like virus (SAEILV) NA tetramer
Components
  • Complex: Siamese algae-eater influenza-like virus (SAEILV) NA tetramer
    • Protein or peptide: Neuraminidase
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

-
Supramolecule #1: Siamese algae-eater influenza-like virus (SAEILV) NA tetramer

SupramoleculeName: Siamese algae-eater influenza-like virus (SAEILV) NA tetramer
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Siamese algae-eater influenza-like virus

-
Macromolecule #1: Neuraminidase

MacromoleculeName: Neuraminidase / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO / EC number: exo-alpha-sialidase
Source (natural)Organism: Siamese algae-eater influenza-like virus
Molecular weightTheoretical: 50.069203 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MLWHCPGSQG TTKWILPSML LAGLLGVSSY LVYSHVSLRL DIAAAVSLIQ NSGNQSSCAA PNPVTVLNQT TVVINTLPVS TSPTYFQPR MSCTGTRFQP FMMMNSPRYG GTGDRGSIHL NREPFVSCSM NECRHFALGH TATQNGPYSA GTGADRSIQR M LFSTKLGE ...String:
MLWHCPGSQG TTKWILPSML LAGLLGVSSY LVYSHVSLRL DIAAAVSLIQ NSGNQSSCAA PNPVTVLNQT TVVINTLPVS TSPTYFQPR MSCTGTRFQP FMMMNSPRYG GTGDRGSIHL NREPFVSCSM NECRHFALGH TATQNGPYSA GTGADRSIQR M LFSTKLGE PFTIDNAIVH MSGWSGSACH DGVEWTYVTV FGTDPDALVK TKYGNNLVDS YRSFAGNILR TQESECVCLN GS CYVMITD GYAGGGGVSQ ARFLVMKQGK IIDVINTSGR SKFTEECTCA ATGNTTIMCA CRDNAYTDRR PIVAIDTIAK TAN VGLMCS PTRMDTPRSA DSAPSSCNVD DGTGGGGVKG GFAVVRRPNG NQFYYTRTGS ASSRVGMEVR GPQTEDPMTG TSAI PLLDI IVSTSVNTGY SSSFEMKGIE CDTPCFVVEH IRSNTWTTAS SSIYCLSGDA SMFQFDDGVN PTA

UniProtKB: Neuraminidase

-
Macromolecule #2: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 2 / Number of copies: 4 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.4 mg/mL
BufferpH: 7.4
Component:
ConcentrationFormulaName
50.0 mMTrisTris
100.0 mMNaClSodium chloride
0.1 %Octyl-beta-GlucosideOctyl-beta-Glucoside
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 47.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.8 µm

+
Image processing

CTF correctionSoftware - Name: cryoSPARC (ver. 4.0) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL / Details: CryoSPARC Ab-initio
Final reconstructionApplied symmetry - Point group: C4 (4 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.75 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.0) / Number images used: 65094
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more