+Open data
-Basic information
Entry | Database: PDB / ID: 8q30 | ||||||
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Title | Sulfolobus acidocaldarius AAP filament. | ||||||
Components | DUF4352 domain-containing protein | ||||||
Keywords | PROTEIN FIBRIL / cell surface appendage / N-glycosylation | ||||||
Function / homology | Immunoglobulin-like fold / membrane / DUF4352 domain-containing protein Function and homology information | ||||||
Biological species | Sulfolobus acidocaldarius (acidophilic) | ||||||
Method | ELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.22 Å | ||||||
Authors | Isupov, M.N. / Gaines, M. / Daum, B. / McLaren, M. | ||||||
Funding support | European Union, 1items
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Citation | Journal: Nat Commun / Year: 2024 Title: CryoEM reveals the structure of an archaeal pilus involved in twitching motility. Authors: Matthew C Gaines / Shamphavi Sivabalasarma / Michail N Isupov / Risat Ul Haque / Mathew McLaren / Cyril Hanus / Vicki A M Gold / Sonja-Verena Albers / Bertram Daum / Abstract: Amongst the major types of archaeal filaments, several have been shown to closely resemble bacterial homologues of the Type IV pili (T4P). Within Sulfolobales, member species encode for three types ...Amongst the major types of archaeal filaments, several have been shown to closely resemble bacterial homologues of the Type IV pili (T4P). Within Sulfolobales, member species encode for three types of T4P, namely the archaellum, the UV-inducible pilus system (Ups) and the archaeal adhesive pilus (Aap). Whereas the archaellum functions primarily in swimming motility, and the Ups in UV-induced cell aggregation and DNA-exchange, the Aap plays an important role in adhesion and twitching motility. Here, we present a cryoEM structure of the Aap of the archaeal model organism Sulfolobus acidocaldarius. We identify the component subunit as AapB and find that while its structure follows the canonical T4P blueprint, it adopts three distinct conformations within the pilus. The tri-conformer Aap structure that we describe challenges our current understanding of pilus structure and sheds new light on the principles of twitching motility. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8q30.cif.gz | 1.8 MB | Display | PDBx/mmCIF format |
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PDB format | pdb8q30.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 8q30.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8q30_validation.pdf.gz | 2.8 MB | Display | wwPDB validaton report |
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Full document | 8q30_full_validation.pdf.gz | 2.9 MB | Display | |
Data in XML | 8q30_validation.xml.gz | 237.4 KB | Display | |
Data in CIF | 8q30_validation.cif.gz | 383.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q3/8q30 ftp://data.pdbj.org/pub/pdb/validation_reports/q3/8q30 | HTTPS FTP |
-Related structure data
Related structure data | 18119MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 14177.022 Da / Num. of mol.: 72 / Source method: isolated from a natural source / Source: (natural) Sulfolobus acidocaldarius (acidophilic) / References: UniProt: A0A0U3GLH8 #2: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source #3: Polysaccharide | 6-deoxy-6-sulfo-beta-D-glucopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2- ...6-deoxy-6-sulfo-beta-D-glucopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Type: oligosaccharide / Mass: 650.606 Da / Num. of mol.: 48 Source method: isolated from a genetically manipulated source #4: Sugar | ChemComp-NAG / Has ligand of interest | N | |
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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 |
-Sample preparation
Component | Name: Filament / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: #1 / Source: NATURAL |
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Source (natural) | Organism: Sulfolobus acidocaldarius (acidophilic) |
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 |
-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: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm |
Image recording | Electron dose: 42.33 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of real images: 6272 |
-Processing
EM software | Name: REFMAC / Version: 5.8.0267 / Category: model refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Helical symmerty | Angular rotation/subunit: -39.879 ° / Axial rise/subunit: 15.403 Å / Axial symmetry: C1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.22 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 947729 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | Resolution: 3.22→3.22 Å / Cor.coef. Fo:Fc: 0.838 / SU B: 7.068 / SU ML: 0.116 / ESU R: 0.112 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
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Solvent computation | Solvent model: PARAMETERS FOR MASK CACLULATION | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 74.836 Å2
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Refinement step | Cycle: 1 / Total: 77784 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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