+Open data
-Basic information
Entry | Database: PDB / ID: 8tj2 | ||||||
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Title | CryoEM structure of Myxococcus xanthus type IV pilus | ||||||
Components | Type IV major pilin protein PilA | ||||||
Keywords | CELL ADHESION / filament / helical reconstruction / CryoEM | ||||||
Function / homology | Type IV pilin PilA / Type IV pilin PilA / Prokaryotic N-terminal methylation site. / Prokaryotic N-terminal methylation motif / Prokaryotic N-terminal methylation site / Pilin-like / pilus / membrane / Type IV major pilin protein PilA Function and homology information | ||||||
Biological species | Myxococcus xanthus DK 1622 (bacteria) | ||||||
Method | ELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3 Å | ||||||
Authors | Zheng, W. / Egelman, E.H. | ||||||
Funding support | United States, 1items
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Citation | Journal: Proc Natl Acad Sci U S A / Year: 2024 Title: Tight-packing of large pilin subunits provides distinct structural and mechanical properties for the type IVa pilus. Authors: Anke Treuner-Lange / Weili Zheng / Albertus Viljoen / Steffi Lindow / Marco Herfurth / Yves F Dufrêne / Lotte Søgaard-Andersen / Edward H Egelman / Abstract: Type IVa pili (T4aP) are ubiquitous cell surface filaments important for surface motility, adhesion to surfaces, DNA uptake, biofilm formation, and virulence. T4aP are built from thousands of copies ...Type IVa pili (T4aP) are ubiquitous cell surface filaments important for surface motility, adhesion to surfaces, DNA uptake, biofilm formation, and virulence. T4aP are built from thousands of copies of the major pilin subunit and tipped by a complex composed of minor pilins and in some systems also the PilY1 adhesin. While major pilins of structurally characterized T4aP have lengths of <165 residues, the major pilin PilA of is unusually large with 208 residues. All major pilins have a conserved N-terminal domain and a variable C-terminal domain, and the additional residues of PilA are due to a larger C-terminal domain. We solved the structure of the T4aP (T4aP) at a resolution of 3.0 Å using cryo-EM. The T4aP follows the structural blueprint of other T4aP with the pilus core comprised of the interacting N-terminal α1-helices, while the globular domains decorate the T4aP surface. The atomic model of PilA built into this map shows that the large C-terminal domain has more extensive intersubunit contacts than major pilins in other T4aP. As expected from these greater contacts, the bending and axial stiffness of the T4aP is significantly higher than that of other T4aP and supports T4aP-dependent motility on surfaces of different stiffnesses. Notably, T4aP variants with interrupted intersubunit interfaces had decreased bending stiffness, pilus length, and strongly reduced motility. These observations support an evolutionary scenario whereby the large major pilin enables the formation of a rigid T4aP that expands the environmental conditions in which the T4aP system functions. #1: Journal: bioRxiv / Year: 2023 Title: Large pilin subunits provide distinct structural and mechanical properties for the type IV pilus. Authors: Anke Treuner-Lange / Weili Zheng / Albertus Viljoen / Steffi Lindow / Marco Herfurth / Yves F Dufrêne / Lotte Søgaard-Andersen / Edward H Egelman Abstract: Type IV pili (T4P) are ubiquitous bacterial cell surface filaments important for surface motility, adhesion to biotic and abiotic surfaces, DNA uptake, biofilm formation, and virulence. T4P are built ...Type IV pili (T4P) are ubiquitous bacterial cell surface filaments important for surface motility, adhesion to biotic and abiotic surfaces, DNA uptake, biofilm formation, and virulence. T4P are built from thousands of copies of the major pilin subunit and tipped by a complex composed of minor pilins and in some systems also the PilY1 adhesin. While the major pilins of structurally characterized T4P have lengths of up to 161 residues, the major pilin PilA of is unusually large with 208 residues. All major pilins have a highly conserved N-terminal domain and a highly variable C-terminal domain, and the additional residues in the PilA are due to a larger C-terminal domain. We solved the structure of the T4P (T4P ) at a resolution of 3.0 Å using cryo-electron microscopy (cryo-EM). The T4P follows the structural blueprint observed in other T4P with the pilus core comprised of the extensively interacting N-terminal α1-helices while the globular domains decorate the T4P surface. The atomic model of PilA built into this map shows that the large C-terminal domain has much more extensive intersubunit contacts than major pilins in other T4P. As expected from these greater contacts, the bending and axial stiffness of the T4P is significantly higher than that of other T4P and supports T4P-dependent motility on surfaces of different stiffnesses. Notably, T4P variants with interrupted intersubunit interfaces had decreased bending stiffness and strongly reduced motility on all surfaces. These observations support an evolutionary scenario whereby the large major pilin enables the formation of a rigid T4P that expands the environmental conditions in which the T4P system functions. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8tj2.cif.gz | 1.2 MB | Display | PDBx/mmCIF format |
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PDB format | pdb8tj2.ent.gz | 1 MB | Display | PDB format |
PDBx/mmJSON format | 8tj2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8tj2_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 8tj2_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 8tj2_validation.xml.gz | 101.2 KB | Display | |
Data in CIF | 8tj2_validation.cif.gz | 148.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tj/8tj2 ftp://data.pdbj.org/pub/pdb/validation_reports/tj/8tj2 | HTTPS FTP |
-Related structure data
Related structure data | 41298MC 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: 21932.318 Da / Num. of mol.: 18 / Source method: isolated from a natural source / Source: (natural) Myxococcus xanthus DK 1622 (bacteria) / References: UniProt: Q59589 |
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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: Myxococcus xanthus type IV pilus / Type: COMPLEX / Entity ID: all / Source: NATURAL |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: Myxococcus xanthus DK 1622 (bacteria) |
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
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 |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 55 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
Helical symmerty | Angular rotation/subunit: 100.7 ° / Axial rise/subunit: 10 Å / Axial symmetry: C1 | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1300000 / Symmetry type: HELICAL | ||||||||||||||||||||||||
Refine LS restraints |
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