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- EMDB-19905: Halobacterium salinarum archaellum filament -

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Basic information

Entry
Database: EMDB / ID: EMD-19905
TitleHalobacterium salinarum archaellum filament
Map data
Sample
  • Organelle or cellular component: Archaellum filament
    • Protein or peptide: Archaellin
Keywordsarchaellum / haloarcheon / archaellin / STRUCTURAL PROTEIN
Biological speciesHalobacterium salinarum (Halophile)
Methodhelical reconstruction / cryo EM / Resolution: 3.23 Å
AuthorsGrossman-Haham I / Shahar A
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat Commun / Year: 2024
Title: Perturbed N-glycosylation of Halobacterium salinarum archaellum filaments leads to filament bundling and compromised cell motility.
Authors: Shahar Sofer / Zlata Vershinin / Leen Mashni / Ran Zalk / Anat Shahar / Jerry Eichler / Iris Grossman-Haham /
Abstract: The swimming device of archaea-the archaellum-presents asparagine (N)-linked glycans. While N-glycosylation serves numerous roles in archaea, including enabling their survival in extreme ...The swimming device of archaea-the archaellum-presents asparagine (N)-linked glycans. While N-glycosylation serves numerous roles in archaea, including enabling their survival in extreme environments, how this post-translational modification contributes to cell motility remains under-explored. Here, we report the cryo-EM structure of archaellum filaments from the haloarchaeon Halobacterium salinarum, where archaellins, the building blocks of the archaellum, are N-glycosylated, and the N-glycosylation pathway is well-resolved. We further determined structures of archaellum filaments from two N-glycosylation mutant strains that generate truncated glycans and analyzed their motility. While cells from the parent strain exhibited unidirectional motility, the N-glycosylation mutant strain cells swam in ever-changing directions within a limited area. Although these mutant strain cells presented archaellum filaments that were highly similar in architecture to those of the parent strain, N-linked glycan truncation greatly affected interactions between archaellum filaments, leading to dramatic clustering of both isolated and cell-attached filaments. We propose that the N-linked tetrasaccharides decorating archaellins act as physical spacers that minimize the archaellum filament aggregation that limits cell motility.
History
DepositionMar 21, 2024-
Header (metadata) releaseJul 17, 2024-
Map releaseJul 17, 2024-
UpdateOct 23, 2024-
Current statusOct 23, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_19905.png

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Map

FileDownload / File: emd_19905.map.gz / Format: CCP4 / Size: 274.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
0.89 Å/pix.
x 416 pix.
= 370.24 Å		0.89 Å/pix.
x 416 pix.
= 370.24 Å		0.89 Å/pix.
x 416 pix.
= 370.24 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.89 Å
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Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.12
Minimum - Maximum-0.34614164 - 0.5440301
Average (Standard dev.)0.00093215716 (±0.020173823)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions416416416
Spacing416416416
CellA=B=C: 370.24 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #2

Fileemd_19905_additional_1.map
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Additional map: #1

Fileemd_19905_additional_2.map
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Half map: #2

Fileemd_19905_half_map_1.map
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Half map: #1

Fileemd_19905_half_map_2.map
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Sample components

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Entire : Archaellum filament

EntireName: Archaellum filament
Components
  • Organelle or cellular component: Archaellum filament
    • Protein or peptide: Archaellin

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Supramolecule #1: Archaellum filament

SupramoleculeName: Archaellum filament / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Halobacterium salinarum (Halophile)
Molecular weightTheoretical: 21.5 KDa

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Macromolecule #1: Archaellin

MacromoleculeName: Archaellin / type: protein_or_peptide / ID: 1
Details: Since Hbt. salinarum encodes five archaellins (i.e., FlaA1, FlaA2, FlaB1, FlaB2, and FlaB3) and their arrangement within the archaellum filaments is unknown, we further refined the cryo-EM ...Details: Since Hbt. salinarum encodes five archaellins (i.e., FlaA1, FlaA2, FlaB1, FlaB2, and FlaB3) and their arrangement within the archaellum filaments is unknown, we further refined the cryo-EM map without applying symmetry, in an attempt to resolve the positions of these archaellins within the filament, as done previously with reconstruction of the Methanocaldococcus villosus archaellum. Symmetry-free refinement improved the overall resolution map to 3.1 A and revealed differences in density among archaellin subunits. Nonetheless, we were unable to identify features that would allow us to unambiguously assign specific archaellins into the density, perhaps because the regions that distinguish each archaellin are few, short, and mostly predicted to lack defined secondary structure, or because the five archaellins are not organized in a repeating pattern. Consequently, we built a model into the central region of the cryo-EM map comprising 26 archaellin subunits that share a consensus sequence, in which identical residues among the five archaellins are explicitly modelled, with those variable residues usually being modelled as alanine residues (UNK).
Number of copies: 26 / Enantiomer: LEVO
Source (natural)Organism: Halobacterium salinarum (Halophile)
Molecular weightTheoretical: 20.107971 KDa
SequenceString: MFEFITDEDE RGQVGIGTLI VFIAMVLVAA IAAGVLINTA GYLQSKGSAT GEEASAQVSN RINIVSAYGN V(UNK) (UNK)(UNK)(UNK)VDYV NLTVRQAAGA DNINL(UNK)KSTI QWIGPD(UNK)ATT LTY(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK) ...String:
MFEFITDEDE RGQVGIGTLI VFIAMVLVAA IAAGVLINTA GYLQSKGSAT GEEASAQVSN RINIVSAYGN V(UNK) (UNK)(UNK)(UNK)VDYV NLTVRQAAGA DNINL(UNK)KSTI QWIGPD(UNK)ATT LTY(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)ENFTT(UNK)S IKG(UNK)(UNK)(UNK)(UNK)VLV DQSDRIKVIM YA(UNK) (UNK)V(UNK)(UNK)(UNK)L (UNK)(UNK)G(UNK)EVQLTV TTQYGSKTTY WAQVPESLKD KNAV(UNK)L

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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: 7.5
Component:
ConcentrationFormulaName
250.0 mg/mLNaClSodium Chloride
20.0 mg/mLMgSO4*7H2OMagnesium Sulfate
3.0 mg/mLNa3C6H5O7sodium citrate
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 30.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: OTHER / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.5 µm

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 5.49 Å
Applied symmetry - Helical parameters - Δ&Phi: 107.95 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 3.23 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 334202
Startup modelType of model: INSILICO MODEL
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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