[English] 日本語
Yorodumi
- EMDB-52629: Structure of the bacterial archaellum from L. aerophila -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-52629
TitleStructure of the bacterial archaellum from L. aerophila
Map data
Sample
  • Organelle or cellular component: Archaellum filament of L. aerophila
    • Protein or peptide: Flagellin
KeywordsHelical / cell surface structure / motility / archaellum / PROTEIN FIBRIL
Function / homologyFlagellin, archaea / Archaebacterial flagellin / Flagellin/pilin, N-terminal / archaeal or bacterial-type flagellum-dependent cell motility / structural molecule activity / membrane / Flagellin
Function and homology information
Biological speciesLitorilinea aerophila (bacteria)
Methodhelical reconstruction / cryo EM / Resolution: 2.7 Å
AuthorsSivabalasarma S / Taib N / Mollat CL / Joest M / Steimle S / Gribaldo S / Albers S-V
Funding support Germany, 1 items
OrganizationGrant numberCountry
German Research Foundation (DFG)403222702 Germany
CitationJournal: Biorxiv / Year: 2025
Title: Horizontal gene transfer of the functional archaellum machinery to Bacteria
Authors: Sivabalasarma S / Taib N / Mollat CL / Joest M / Steimle S / Gribaldo S / Albers SV
History
DepositionJan 28, 2025-
Header (metadata) releaseMay 21, 2025-
Map releaseMay 21, 2025-
UpdateMay 21, 2025-
Current statusMay 21, 2025Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_52629.png

Downloads & links

-
Map

FileDownload / File: emd_52629.map.gz / Format: CCP4 / Size: 63.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.96 Å/pix.
x 255 pix.
= 244.8 Å		0.96 Å/pix.
x 255 pix.
= 244.8 Å		0.96 Å/pix.
x 255 pix.
= 244.8 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: 0.023
Minimum - Maximum-0.025510956 - 0.059709243
Average (Standard dev.)0.0004965826 (±0.0038878853)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions255255255
Spacing255255255
CellA=B=C: 244.79999 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #2

Fileemd_52629_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_52629_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Archaellum filament of L. aerophila

EntireName: Archaellum filament of L. aerophila
Components
  • Organelle or cellular component: Archaellum filament of L. aerophila
    • Protein or peptide: Flagellin

-
Supramolecule #1: Archaellum filament of L. aerophila

SupramoleculeName: Archaellum filament of L. aerophila / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all
Details: Archaellum filament isolated from the cell surface of L. aerophila
Source (natural)Organism: Litorilinea aerophila (bacteria) / Strain: DSM:25763 / Location in cell: cell surface

-
Macromolecule #1: Flagellin

MacromoleculeName: Flagellin / type: protein_or_peptide / ID: 1 / Number of copies: 17 / Enantiomer: LEVO
Source (natural)Organism: Litorilinea aerophila (bacteria) / Strain: DSM:25763
Molecular weightTheoretical: 19.468656 KDa
SequenceString:
ITALETAIIL IAFVVVASVF AFTILSAGTF STERGKEAVY AGLSEVRSSI EIKGSVVIIG ETTGATGTVD SVIFTVASAA GGEPIDLNN DPDDRVVVID YRDATQRHTD VDWSVTWLGK NDYDTTGDTL LEQGELAEIT VTLAPTITLS TNTDFIIEVK P PAGAVFSI QRTTPAYIET VNDLQ

UniProtKB: Flagellin

-
Experimental details

-
Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

-
Sample preparation

BufferpH: 7.4
Component:
ConcentrationFormulaName
2.0 %NaClsodium chloride
1.0 xPBSphosphate buffered saline

Details: 2% NaCl in 1x PBS, pH 7.4
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 295.15 K / Instrument: FEI VITROBOT MARK IV
Detailssheared and purified archaella filament from L. aerophila

-
Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: TFS Selectris / Energy filter - Slit width: 10 eV
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Calibrated magnification: 130000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.5 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Final reconstructionNumber classes used: 20
Applied symmetry - Helical parameters - Δz: 5.64 Å
Applied symmetry - Helical parameters - Δ&Phi: 108.14 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. v4.6) / Number images used: 1610077
CTF correctionType: NONE
Startup modelType of model: OTHER
Final angle assignmentType: NOT APPLICABLE
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