[English] 日本語
Yorodumi
- EMDB-53449: Cryo-electron tomography of an A549 cell infected with influenza ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-53449
TitleCryo-electron tomography of an A549 cell infected with influenza A/WSN/33 virus
Map dataCryo-electron tomogram of filamentous influenza A virus (WSN-M1-Udorn) particles in an endosomal compartment of infected A549 cells at 15-30 min post infection.
Sample
  • Virus: Influenza A virus (A/WSN/1933(H1N1))
Keywordsinfluenza A virus entry / VIRUS
Biological speciesInfluenza A virus (A/WSN/1933(H1N1))
Methodelectron tomography / cryo EM
AuthorsPeterl S / Chlanda P
Funding support Germany, 1 items
OrganizationGrant numberCountry
German Research Foundation (DFG)240245660-SFB1129 Germany
CitationJournal: To Be Published
Title: Cryo-electron tomography of an A549 cell infected with influenza A/WSN/33 virus
Authors: Peterl S / Chlanda P
History
DepositionApr 16, 2025-
Header (metadata) releaseApr 29, 2026-
Map releaseApr 29, 2026-
UpdateApr 29, 2026-
Current statusApr 29, 2026Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_53449.png

Downloads & links

-
Map

FileDownload / File: emd_53449.map.gz / Format: CCP4 / Size: 1.2 GB / Type: IMAGE STORED AS SIGNED BYTE
AnnotationCryo-electron tomogram of filamentous influenza A virus (WSN-M1-Udorn) particles in an endosomal compartment of infected A549 cells at 15-30 min post infection.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
8.01 Å/pix.
x 504 pix.
= 4038.552 Å		8.01 Å/pix.
x 1920 pix.
= 15384.959 Å		8.01 Å/pix.
x 1364 pix.
= 10929.731 Å

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 8.013 Å
Density

Histogram

Histogram (log scale)
Minimum - Maximum-128.0 - 127.0
Average (Standard dev.)2.693709 (±21.33286)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-278278-252
Dimensions19201364504
Spacing13641920504
CellA: 10929.731 Å / B: 15384.959 Å / C: 4038.5518 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Sample components

-
Entire : Influenza A virus (A/WSN/1933(H1N1))

EntireName: Influenza A virus (A/WSN/1933(H1N1))
Components
  • Virus: Influenza A virus (A/WSN/1933(H1N1))

-
Supramolecule #1: Influenza A virus (A/WSN/1933(H1N1))

SupramoleculeName: Influenza A virus (A/WSN/1933(H1N1)) / type: virus / ID: 1 / Parent: 0 / NCBI-ID: 382835 / Sci species name: Influenza A virus (A/WSN/1933(H1N1)) / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No

-
Experimental details

-
Structure determination

Methodcryo EM
Processingelectron tomography
Aggregation statecell

-
Sample preparation

BufferpH: 7.4
GridModel: Quantifoil R1/4 / Support film - Material: SILICON DIOXIDE / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE / Chamber humidity: 80 % / Chamber temperature: 310 K / Instrument: LEICA EM GP / Details: GP2.
DetailsM segment from influenza A/Udorn/307/72 virus
SectioningFocused ion beam - Instrument: OTHER / Focused ion beam - Ion: OTHER / Focused ion beam - Voltage: 30 / Focused ion beam - Current: 0.03 / Focused ion beam - Duration: 120 / Focused ion beam - Temperature: 83 K / Focused ion beam - Initial thickness: 1000 / Focused ion beam - Final thickness: 150
Focused ion beam - Details: This applies to the last milling step.. The value given for _em_focused_ion_beam.instrument is Aquilos2 (TermoFisher Scientific). This is not in a list of allowed values ...Focused ion beam - Details: This applies to the last milling step.. The value given for _em_focused_ion_beam.instrument is Aquilos2 (TermoFisher Scientific). This is not in a list of allowed values {'DB235', 'OTHER'} so OTHER is written into the XML file.

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 3.2 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 3.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Final reconstructionNumber images used: 41
CTF correctionType: PHASE FLIPPING ONLY

+
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