[English] 日本語
Yorodumi
- EMDB-52255: Influenza Neuraminidase in complex with N-Acyl Oseltamivir inhibitor -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-52255
TitleInfluenza Neuraminidase in complex with N-Acyl Oseltamivir inhibitor
Map data
Sample
  • Complex: Influenza Neuraminidase in complex with N-Acyl Oseltamivir inhibitor
    • Protein or peptide: Neuraminidase
  • Ligand: (3~{S},4~{R},5~{R},6~{R})-4-acetamido-3-azanyl-6-(butanoylamino)-5-pentan-3-yloxy-cyclohexene-1-carboxylic acid
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: CALCIUM ION
  • Ligand: water
KeywordsInfluenza / Neuraminidase / VIRAL PROTEIN
Function / homology
Function and homology information


exo-alpha-sialidase / exo-alpha-sialidase activity / viral budding from plasma membrane / carbohydrate metabolic process / host cell plasma membrane / virion membrane / metal ion binding / membrane
Similarity search - Function
Sialidase, Influenza viruses A/B / Glycoside hydrolase, family 34 / Neuraminidase / Sialidase superfamily
Similarity search - Domain/homology
Biological speciesInfluenza A virus
Methodsingle particle reconstruction / cryo EM / Resolution: 2.0 Å
AuthorsMoran E / Davies G
Funding supportEuropean Union, 1 items
OrganizationGrant numberCountry
European Research Council (ERC)European Union
CitationJournal: To Be Published
Title: Oseltamivir aziridines are neuraminidase imaging agents and potent anti-influenza agents
Authors: Moran E / Vriends M / Calvelo M / Hansen T / Pickles I / Xin X / Biezeno M / Armstrong Z / Ferras M / Li L / Lilley A / Harvey R / Schroder S / Van der Marel G / Artola M / Aerts J / Blaza J ...Authors: Moran E / Vriends M / Calvelo M / Hansen T / Pickles I / Xin X / Biezeno M / Armstrong Z / Ferras M / Li L / Lilley A / Harvey R / Schroder S / Van der Marel G / Artola M / Aerts J / Blaza J / Rovira C / Codee J / Overkleeft H / Davies G
History
DepositionDec 4, 2024-
Header (metadata) releaseDec 17, 2025-
Map releaseDec 17, 2025-
UpdateDec 17, 2025-
Current statusDec 17, 2025Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_52255.png

Downloads & links

-
Map

FileDownload / File: emd_52255.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.9 Å/pix.
x 200 pix.
= 180. Å		0.9 Å/pix.
x 200 pix.
= 180. Å		0.9 Å/pix.
x 200 pix.
= 180. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.9 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.04
Minimum - Maximum-0.16887158 - 0.33244586
Average (Standard dev.)0.0001768305 (±0.013744034)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 180.0 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_52255_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_52255_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_52255_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Influenza Neuraminidase in complex with N-Acyl Oseltamivir inhibitor

EntireName: Influenza Neuraminidase in complex with N-Acyl Oseltamivir inhibitor
Components
  • Complex: Influenza Neuraminidase in complex with N-Acyl Oseltamivir inhibitor
    • Protein or peptide: Neuraminidase
  • Ligand: (3~{S},4~{R},5~{R},6~{R})-4-acetamido-3-azanyl-6-(butanoylamino)-5-pentan-3-yloxy-cyclohexene-1-carboxylic acid
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: CALCIUM ION
  • Ligand: water

-
Supramolecule #1: Influenza Neuraminidase in complex with N-Acyl Oseltamivir inhibitor

SupramoleculeName: Influenza Neuraminidase in complex with N-Acyl Oseltamivir inhibitor
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Influenza A 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: Influenza A virus
Molecular weightTheoretical: 42.499523 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: VKLAGNSSLC PVSGWAPLSK DNSVRIGSKG DVFVIREPFI SCSPLECRTF FLTQGALLND KHSNGTIKDR SPYRTLMSVP IGSVPSPYN ARFESIAWSA SACHDGINWL TIGITGPDNG AVAILKYNGI ITDTIKSWRN NILRTQESEC ACVNGSCFTV M TDGPSNGQ ...String:
VKLAGNSSLC PVSGWAPLSK DNSVRIGSKG DVFVIREPFI SCSPLECRTF FLTQGALLND KHSNGTIKDR SPYRTLMSVP IGSVPSPYN ARFESIAWSA SACHDGINWL TIGITGPDNG AVAILKYNGI ITDTIKSWRN NILRTQESEC ACVNGSCFTV M TDGPSNGQ ASYKIFRIEK GKIVKSVEMN APNYHYEECS CYPDSSEITC VCRDNWHGSN RPWVSFNQNL EYQIGYICSG IF GDNPRPN DKTGSCGPVS SNGANGVKGF SFKYGNGVWI GRTKSISSRN GFEMIWDPNG WTGTDNNFSI KQDIVGINEW SGY SGSFVM HPELTGLDCI VPCFWVELIR GRPKENTIWT SGSSISFCGV NSDTVGWSWP DGAELPFTID K

UniProtKB: Neuraminidase

-
Macromolecule #2: (3~{S},4~{R},5~{R},6~{R})-4-acetamido-3-azanyl-6-(butanoylamino)-...

MacromoleculeName: (3~{S},4~{R},5~{R},6~{R})-4-acetamido-3-azanyl-6-(butanoylamino)-5-pentan-3-yloxy-cyclohexene-1-carboxylic acid
type: ligand / ID: 2 / Number of copies: 4 / Formula: A1IVX
Molecular weightTheoretical: 369.456 Da

-
Macromolecule #3: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 3 / Number of copies: 4 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

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

-
Macromolecule #4: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 4 / Number of copies: 4 / Formula: CA
Molecular weightTheoretical: 40.078 Da

-
Macromolecule #5: water

MacromoleculeName: water / type: ligand / ID: 5 / Number of copies: 382 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration1.5 mg/mL
BufferpH: 7
Component:
ConcentrationFormulaName
25.0 mMTrisTris
150.0 mMNaClSodium chloride
100.0 mMCaCl2Calcium chloride

Details: 25 mM Tris pH 7.0 150 mM NaCl, 100 mM CaCl2
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 180 sec. / Pretreatment - Atmosphere: OTHER
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV / Details: Blot force -10 and blot time 3 seconds.

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 43.99 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.4000000000000001 µm / Nominal defocus min: 0.6 µm
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionSoftware - Name: CTFFIND / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C4 (4 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 5.0) / Number images used: 216385
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
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