[English] 日本語
Yorodumi
- EMDB-43829: cryo-EM of Cupriavidus gilardii flagellum -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-43829
Titlecryo-EM of Cupriavidus gilardii flagellum
Map datacryo-EM of Cupriavidus gilardii flagellum
Sample
  • Complex: Flagellar filament
    • Protein or peptide: Flagellin
KeywordsFlagellum / Flagellar filament / filament / helical symmetry / PROTEIN FIBRIL
Function / homology
Function and homology information


bacterial-type flagellum / structural molecule activity / extracellular region
Similarity search - Function
Flagellin, C-terminal domain, subdomain 2 / Flagellin, C-terminal domain / Bacterial flagellin C-terminal helical region / Flagellin / Flagellin, N-terminal domain / Bacterial flagellin N-terminal helical region
Similarity search - Domain/homology
Biological speciesCupriavidus gilardii (bacteria)
Methodhelical reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsFields JL / Zhang H / Halder SK / Wu H / Wang F
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM138756 United States
CitationJournal: Nat Commun / Year: 2024
Title: Structural diversity and clustering of bacterial flagellar outer domains.
Authors: Jessie Lynda Fields / Hua Zhang / Nathan F Bellis / Holly A Petersen / Sajal K Halder / Shane T Rich-New / Mart Krupovic / Hui Wu / Fengbin Wang /
Abstract: Supercoiled flagellar filaments function as mechanical propellers within the bacterial flagellum complex, playing a crucial role in motility. Flagellin, the building block of the filament, features a ...Supercoiled flagellar filaments function as mechanical propellers within the bacterial flagellum complex, playing a crucial role in motility. Flagellin, the building block of the filament, features a conserved inner D0/D1 core domain across different bacterial species. In contrast, approximately half of the flagellins possess additional, highly divergent outer domain(s), suggesting varied functional potential. In this study, we report atomic structures of flagellar filaments from three distinct bacterial species: Cupriavidus gilardii, Stenotrophomonas maltophilia, and Geovibrio thiophilus. Our findings reveal that the flagella from the facultative anaerobic G. thiophilus possesses a significantly more negatively charged surface, potentially enabling adhesion to positively charged minerals. Furthermore, we analyze all AlphaFold predicted structures for annotated bacterial flagellins, categorizing the flagellin outer domains into 682 structural clusters. This classification provides insights into the prevalence and experimental verification of these outer domains. Remarkably, two of the flagellar structures reported herein belong to a distinct cluster, indicating additional opportunities on the study of the functional diversity of flagellar outer domains. Our findings underscore the complexity of bacterial flagellins and open up possibilities for future studies into their varied roles beyond motility.
History
DepositionFeb 26, 2024-
Header (metadata) releaseNov 13, 2024-
Map releaseNov 13, 2024-
UpdateMay 28, 2025-
Current statusMay 28, 2025Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_43829.png

Downloads & links

-
Map

FileDownload / File: emd_43829.map.gz / Format: CCP4 / Size: 1000 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationcryo-EM of Cupriavidus gilardii flagellum
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.11 Å/pix.
x 640 pix.
= 710.4 Å		1.11 Å/pix.
x 640 pix.
= 710.4 Å		1.11 Å/pix.
x 640 pix.
= 710.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.11 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.215
Minimum - Maximum-0.4793092 - 0.9507083
Average (Standard dev.)0.0037822202 (±0.028065627)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-320-320-320
Dimensions640640640
Spacing640640640
CellA=B=C: 710.4 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #1

Fileemd_43829_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_43829_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Flagellar filament

EntireName: Flagellar filament
Components
  • Complex: Flagellar filament
    • Protein or peptide: Flagellin

-
Supramolecule #1: Flagellar filament

SupramoleculeName: Flagellar filament / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Cupriavidus gilardii (bacteria)

-
Macromolecule #1: Flagellin

MacromoleculeName: Flagellin / type: protein_or_peptide / ID: 1 / Number of copies: 22 / Enantiomer: LEVO
Source (natural)Organism: Cupriavidus gilardii (bacteria)
Molecular weightTheoretical: 41.336453 KDa
SequenceString: MAQVINTNSL SLMTQNNLNT SQSALNTAIQ RLSSGLRINS AKDDAAGQAI ANRFTANIKG LTQAQRNAND GISLAQTTEG ALTEVNNNL QRIRELSVQA ATGSNSASDL QSIQDEIKQR LEEINRVSEQ TQFNGVKVLA KDTKMNIQVG ANDGEIIAID L KEITAKTL ...String:
MAQVINTNSL SLMTQNNLNT SQSALNTAIQ RLSSGLRINS AKDDAAGQAI ANRFTANIKG LTQAQRNAND GISLAQTTEG ALTEVNNNL QRIRELSVQA ATGSNSASDL QSIQDEIKQR LEEINRVSEQ TQFNGVKVLA KDTKMNIQVG ANDGEIIAID L KEITAKTL GLDGFNVSGP KGTPAALVAA DYQAAYGTTT NVTTTAVTES SANALAGRLG VANGSVALAA TAEKDDNGNW YA TVTITAG SATEVSTLKA KGFEVENGVA KEFYIALDPQ SADVTTTAGT AAFALDTANI QLSSITSGAS SNPLAKLDAA LAD VDTLRS SLGAVQNRFD SVISNLGTTV TNLSASRSRI QDADYATEVS NMTRAQILQQ AGTSVLAQAN QTTQNVLSLL R

UniProtKB: Flagellin

-
Experimental details

-
Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

-
Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 110.25 Å
Applied symmetry - Helical parameters - Δ&Phi: -0.61 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF
Details: The helical symmetry was relaxed in the final reconstruction
Number images used: 223582
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final angle assignmentType: NOT APPLICABLE

+
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