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Open data
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Basic information
Entry | Database: PDB / ID: 7pnb | ||||||
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Title | Sulfolobus acidocaldarius 0406 filament. | ||||||
![]() | Sulfolobus acidocaldarius 0406 filament. | ||||||
![]() | PROTEIN FIBRIL / cell surface appendage / beta-strand addition / isopeptide bond / N-glycosylation / beta-sandwich | ||||||
Function / homology | Uncharacterized protein![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.46 Å | ||||||
![]() | Isupov, M.N. / Gaines, M. / Daum, B. | ||||||
Funding support | European Union, 1items
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![]() | ![]() Title: Electron cryo-microscopy reveals the structure of the archaeal thread filament. Authors: Matthew C Gaines / Michail N Isupov / Shamphavi Sivabalasarma / Risat Ul Haque / Mathew McLaren / Clara L Mollat / Patrick Tripp / Alexander Neuhaus / Vicki A M Gold / Sonja-Verena Albers / Bertram Daum / ![]() ![]() Abstract: Pili are filamentous surface extensions that play roles in bacterial and archaeal cellular processes such as adhesion, biofilm formation, motility, cell-cell communication, DNA uptake and horizontal ...Pili are filamentous surface extensions that play roles in bacterial and archaeal cellular processes such as adhesion, biofilm formation, motility, cell-cell communication, DNA uptake and horizontal gene transfer. The model archaeaon Sulfolobus acidocaldarius assembles three filaments of the type-IV pilus superfamily (archaella, archaeal adhesion pili and UV-inducible pili), as well as a so-far uncharacterised fourth filament, named "thread". Here, we report on the cryo-EM structure of the archaeal thread. The filament is highly glycosylated and consists of subunits of the protein Saci_0406, arranged in a head-to-tail manner. Saci_0406 displays structural similarity, but low sequence homology, to bacterial type-I pilins. Thread subunits are interconnected via donor strand complementation, a feature reminiscent of bacterial chaperone-usher pili. However, despite these similarities in overall architecture, archaeal threads appear to have evolved independently and are likely assembled by a distinct mechanism. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 385.7 KB | Display | ![]() |
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PDB format | ![]() | 342.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 4.4 MB | Display | ![]() |
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Full document | ![]() | 4.4 MB | Display | |
Data in XML | ![]() | 57.7 KB | Display | |
Data in CIF | ![]() | 84.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 13546MC M: map data used to model this data C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Components
#1: Protein | Mass: 22291.539 Da / Num. of mol.: 9 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: ATZ20_07285 / Production host: ![]() ![]() #2: Polysaccharide | beta-D-glucopyranose-(1-4)-6-deoxy-6-sulfo-beta-D-glucopyranose-(1-3)-[alpha-D-mannopyranose-(1-4)] ...beta-D-glucopyranose-(1-4)-6-deoxy-6-sulfo-beta-D-glucopyranose-(1-3)-[alpha-D-mannopyranose-(1-4)][alpha-D-mannopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Type: oligosaccharide / Mass: 1137.028 Da / Num. of mol.: 36 Source method: isolated from a genetically manipulated source #3: Polysaccharide | 6-deoxy-6-sulfo-beta-D-glucopyranose-(1-3)-[alpha-D-mannopyranose-(1-4)]2-acetamido-2-deoxy-beta-D- ...6-deoxy-6-sulfo-beta-D-glucopyranose-(1-3)-[alpha-D-mannopyranose-(1-4)]2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Type: oligosaccharide / Mass: 812.746 Da / Num. of mol.: 9 Source method: isolated from a genetically manipulated source Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: FILAMENT / 3D reconstruction method: helical reconstruction |
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Sample preparation
Component | Name: Filament / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: #1 / Source: NATURAL |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: ![]() ![]() |
Buffer solution | pH: 3 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES Details: Mixed population of filaments isolated from Sulfolobus acidocaldarius |
Vitrification | Cryogen name: ETHANE |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 42.33 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 6272 |
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Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Helical symmerty | Angular rotation/subunit: -103.234 ° / Axial rise/subunit: 31.649 Å / Axial symmetry: C1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 410270 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.46 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 188620 / Num. of class averages: 1 / Symmetry type: HELICAL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: AB INITIO MODEL / Space: RECIPROCAL Details: Jligand was used for preparing dictionaries for an unusual sugars and an isopeptide link beween main chain nitrogen of the N-terminal D25 and C gamma of N57 from N-2 monomer in the filament. |