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- EMDB-43868: Cryo-EM of Geovibrio thiophilus flagellum -

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Basic information

Entry
Database: EMDB / ID: EMD-43868
TitleCryo-EM of Geovibrio thiophilus flagellum
Map dataCryo-EM of Geovibrio thiophilus 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 speciesGeovibrio thiophilus (bacteria)
Methodhelical reconstruction / cryo EM / Resolution: 4.1 Å
AuthorsPetersen HA / Fields JL / 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 28, 2024-
Header (metadata) releaseNov 13, 2024-
Map releaseNov 13, 2024-
UpdateMay 28, 2025-
Current statusMay 28, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_43868.png

Downloads & links

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Map

FileDownload / File: emd_43868.map.gz / Format: CCP4 / Size: 1000 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM of Geovibrio thiophilus 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: 3.45
Minimum - Maximum-0.23871866 - 11.888287
Average (Standard dev.)0.077688135 (±0.6350565)
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 °

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Supplemental data

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Half map: #1

Fileemd_43868_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_43868_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Flagellar filament

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

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Supramolecule #1: Flagellar filament

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

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Macromolecule #1: Flagellin

MacromoleculeName: Flagellin / type: protein_or_peptide / ID: 1 / Number of copies: 22 / Enantiomer: LEVO
Source (natural)Organism: Geovibrio thiophilus (bacteria)
Molecular weightTheoretical: 83.045672 KDa
SequenceString: MAMYINTNVP SLTAQRYLGE TNNAVSKSLE RLSSGLRINS ASDDASGLAI SEKLRGQISG LKRASLNAQD GISLLQTAEG GLQNIQDML QRMRELAVQA GNGVYTTNDR AEIQKEVDQL KEEINRIASS TEFNTKKLLN GDSTALWSSD SSDLDVVIKS A VAEGNYNL ...String:
MAMYINTNVP SLTAQRYLGE TNNAVSKSLE RLSSGLRINS ASDDASGLAI SEKLRGQISG LKRASLNAQD GISLLQTAEG GLQNIQDML QRMRELAVQA GNGVYTTNDR AEIQKEVDQL KEEINRIASS TEFNTKKLLN GDSTALWSSD SSDLDVVIKS A VAEGNYNL NVTVDPGKNF VYKSDVMTLN EDAIGAEIVT AGGDVNETNV GFVTDPNTLA STGTAYYTVD VTAGADTLSS VA TMSVYRQ AGSNFGSVAT WTTGGTVADS GYLLIEAQEN FTVSAGTTAN YTFKATFVDA KTGEKSTYEI EGGDDGAGNL VFD LADMTG AGFSGEVSIA IGTDANMQSG DKILLSTTEA VDTSATSGGG TIAISGGPAG TTGAIISYGN NELTKVDNGD TTID YNSVT VYHAALNVET GNLDVGNLTF NFREDTGTDT AYGSTTGGSF DLLVAGGGEA ATSTTKLKDI SRFTTDDGVN IFAAG PQEL TIFGNGSSAT IYLEGDDTVS EFETKLSSAI LELGMGATAG TSDEAATVNS NLVNYVSTGD VTDSSNEALA GTFVIQ TAR LGDDSKLSFI GDQNLINALS LATIQEGENS ETTIKVTDAH TGKFIGSDSV NDSTLRGVIQ GVDVKIDSDV GVSISWN ST KKTMEFSATG ESEDIKLHLV DNAMEMQIGA NEGQTILANI PQVDTTSLGI DDILMVDQEL AQESITKLDK ALETVSGV R ATIGAQINRL EYTMTGLDTT RENLTAAESR IRDLDIADEM AKFTKNQILA QSNISMLAQA NSLPQMALSL LG

UniProtKB: Flagellin

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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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

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 111.12 Å
Applied symmetry - Helical parameters - Δ&Phi: -0.30 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 21618
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final angle assignmentType: NOT APPLICABLE

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