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Yorodumi- PDB-9esm: Archaellum filament from the Halobacterium salinarum deltaAgl26 strain -
+Open data
-Basic information
Entry | Database: PDB / ID: 9esm | ||||||
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Title | Archaellum filament from the Halobacterium salinarum deltaAgl26 strain | ||||||
Components | Archaellin | ||||||
Keywords | STRUCTURAL PROTEIN / archaellum / haloarcheon / archaellin | ||||||
Biological species | Halobacterium salinarum (Halophile) | ||||||
Method | ELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.06 Å | ||||||
Authors | Grosmann-Haham, I. / Shahar, A. | ||||||
Funding support | 1items
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Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 9esm.cif.gz | 784.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb9esm.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 9esm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 9esm_validation.pdf.gz | 4.1 MB | Display | wwPDB validaton report |
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Full document | 9esm_full_validation.pdf.gz | 4.1 MB | Display | |
Data in XML | 9esm_validation.xml.gz | 114.3 KB | Display | |
Data in CIF | 9esm_validation.cif.gz | 179 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/es/9esm ftp://data.pdbj.org/pub/pdb/validation_reports/es/9esm | HTTPS FTP |
-Related structure data
Related structure data | 19943MC 9eq7C 9etuC M: map data used to model this data C: citing same article (ref.) |
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-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 20107.971 Da / Num. of mol.: 25 / Source method: isolated from a natural source 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). Source: (natural) Halobacterium salinarum (Halophile) #2: Polysaccharide | beta-D-glucopyranuronic acid-(1-4)-beta-D-glucopyranose Type: oligosaccharide / Mass: 356.280 Da / Num. of mol.: 50 / Source method: obtained synthetically Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: HELICAL ARRAY / 3D reconstruction method: helical reconstruction |
-Sample preparation
Component | Name: Archaellum filament / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: #1 / Source: NATURAL |
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Molecular weight | Value: 0.0187 MDa / Experimental value: NO |
Source (natural) | Organism: Halobacterium salinarum (Halophile) |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Microscopy | Model: TFS GLACIOS |
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Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: SPOT SCAN |
Electron lens | Mode: OTHER / Nominal defocus max: 1500 nm / Nominal defocus min: 500 nm |
Image recording | Electron dose: 30 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) |
-Processing
EM software | Name: PHENIX / Version: 1.21rc1_4985: / Category: model refinement | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
Helical symmerty | Angular rotation/subunit: 107.91 ° / Axial rise/subunit: 5.45 Å / Axial symmetry: C1 | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.06 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 448635 / Symmetry type: HELICAL | ||||||||||||||||||||||||
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