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- EMDB-26158: Cryo-EM of A. pernix flagellum -

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Basic information

Entry
Database: EMDB / ID: EMD-26158
TitleCryo-EM of A. pernix flagellum
Map dataCryo-EM of A. pernix flagellum
Sample
  • Complex: A. pernix flagellum
    • Protein or peptide: Probable flagellin 1
Keywordshelical symmetry / flagellum / cell appendage / STRUCTURAL PROTEIN
Function / homologyarchaeal-type flagellum / Flagellin/pilin, N-terminal / Flagellin, archaea / Archaebacterial flagellin / archaeal or bacterial-type flagellum-dependent cell motility / structural molecule activity / Probable flagellin 1
Function and homology information
Biological speciesAeropyrum pernix (archaea)
Methodhelical reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsWang F / Cvirkaite-Krupovic V
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM122510 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)K99GM138756 United States
CitationJournal: Proc Natl Acad Sci U S A / Year: 2023
Title: The evolution of archaeal flagellar filaments.
Authors: Mark A B Kreutzberger / Virginija Cvirkaite-Krupovic / Ying Liu / Diana P Baquero / Junfeng Liu / Ravi R Sonani / Chris R Calladine / Fengbin Wang / Mart Krupovic / Edward H Egelman /
Abstract: Flagellar motility has independently arisen three times during evolution: in bacteria, archaea, and eukaryotes. In prokaryotes, the supercoiled flagellar filaments are composed largely of a single ...Flagellar motility has independently arisen three times during evolution: in bacteria, archaea, and eukaryotes. In prokaryotes, the supercoiled flagellar filaments are composed largely of a single protein, bacterial or archaeal flagellin, although these two proteins are not homologous, while in eukaryotes, the flagellum contains hundreds of proteins. Archaeal flagellin and archaeal type IV pilin are homologous, but how archaeal flagellar filaments (AFFs) and archaeal type IV pili (AT4Ps) diverged is not understood, in part, due to the paucity of structures for AFFs and AT4Ps. Despite having similar structures, AFFs supercoil, while AT4Ps do not, and supercoiling is essential for the function of AFFs. We used cryo-electron microscopy to determine the atomic structure of two additional AT4Ps and reanalyzed previous structures. We find that all AFFs have a prominent 10-strand packing, while AT4Ps show a striking structural diversity in their subunit packing. A clear distinction between all AFF and all AT4P structures involves the extension of the N-terminal α-helix with polar residues in the AFFs. Additionally, we characterize a flagellar-like AT4P from with filament and subunit structure similar to that of AFFs which can be viewed as an evolutionary link, showing how the structural diversity of AT4Ps likely allowed for an AT4P to evolve into a supercoiling AFF.
History
DepositionFeb 9, 2022-
Header (metadata) releaseJun 1, 2022-
Map releaseJun 1, 2022-
UpdateAug 16, 2023-
Current statusAug 16, 2023Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_26158.png

Downloads & links

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Map

FileDownload / File: emd_26158.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM of A. pernix flagellum
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 320 pix.
= 345.6 Å		1.08 Å/pix.
x 320 pix.
= 345.6 Å		1.08 Å/pix.
x 320 pix.
= 345.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.08 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.3
Minimum - Maximum-0.365167 - 0.80065286
Average (Standard dev.)0.004914134 (±0.034164436)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-160-160-160
Dimensions320320320
Spacing320320320
CellA=B=C: 345.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : A. pernix flagellum

EntireName: A. pernix flagellum
Components
  • Complex: A. pernix flagellum
    • Protein or peptide: Probable flagellin 1

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Supramolecule #1: A. pernix flagellum

SupramoleculeName: A. pernix flagellum / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Aeropyrum pernix (archaea)

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Macromolecule #1: Probable flagellin 1

MacromoleculeName: Probable flagellin 1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Aeropyrum pernix (archaea)
Molecular weightTheoretical: 21.37159 KDa
SequenceString: MRRRRGIVGI EAAIVLIAFV IVAAALAFVA LNMGLFTTQK SKEVMQRGLE EATSALEVDG SVIANVTSGS VDAIAIPIKV SPGREGVDM SVDKTTVRVM LPSKFYENAY CGVFDGSSLS DSKLSTITSS IACTTGWAYL VIFNGDGDNV LELGEKGLLV L ELPTPLNS ...String:
MRRRRGIVGI EAAIVLIAFV IVAAALAFVA LNMGLFTTQK SKEVMQRGLE EATSALEVDG SVIANVTSGS VDAIAIPIKV SPGREGVDM SVDKTTVRVM LPSKFYENAY CGVFDGSSLS DSKLSTITSS IACTTGWAYL VIFNGDGDNV LELGEKGLLV L ELPTPLNS YEEFKVEVRP VQGAALTVER IVPASLPTGG AVSLG

UniProtKB: Probable flagellin 1

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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: 6
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.5 µm
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final angle assignmentType: NOT APPLICABLE
Final reconstructionApplied symmetry - Helical parameters - Δz: 5.52 Å
Applied symmetry - Helical parameters - Δ&Phi: 108 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 59338

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