+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-41298 | |||||||||
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Title | CryoEM structure of Myxococcus xanthus type IV pilus | |||||||||
Map data | ||||||||||
Sample |
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Keywords | filament / helical reconstruction / CryoEM / CELL ADHESION | |||||||||
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 | helical reconstruction / cryo EM / Resolution: 3.0 Å | |||||||||
Authors | Zheng W / Egelman EH | |||||||||
Funding support | United States, 1 items
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Citation | 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
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_41298.map.gz | 6.5 MB | EMDB map data format | |
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Header (meta data) | emd-41298-v30.xml emd-41298.xml | 15.1 KB 15.1 KB | Display Display | EMDB header |
Images | emd_41298.png | 104.2 KB | ||
Filedesc metadata | emd-41298.cif.gz | 5.3 KB | ||
Others | emd_41298_half_map_1.map.gz emd_41298_half_map_2.map.gz | 59.3 MB 59.3 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-41298 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-41298 | HTTPS FTP |
-Validation report
Summary document | emd_41298_validation.pdf.gz | 764.8 KB | Display | EMDB validaton report |
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Full document | emd_41298_full_validation.pdf.gz | 764.4 KB | Display | |
Data in XML | emd_41298_validation.xml.gz | 12.5 KB | Display | |
Data in CIF | emd_41298_validation.cif.gz | 14.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-41298 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-41298 | HTTPS FTP |
-Related structure data
Related structure data | 8tj2MC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_41298.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 1.08 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #1
File | emd_41298_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_41298_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Myxococcus xanthus type IV pilus
Entire | Name: Myxococcus xanthus type IV pilus |
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Components |
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-Supramolecule #1: Myxococcus xanthus type IV pilus
Supramolecule | Name: Myxococcus xanthus type IV pilus / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Myxococcus xanthus DK 1622 (bacteria) |
-Macromolecule #1: Type IV major pilin protein PilA
Macromolecule | Name: Type IV major pilin protein PilA / type: protein_or_peptide / ID: 1 / Number of copies: 18 / Enantiomer: LEVO |
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Source (natural) | Organism: Myxococcus xanthus DK 1622 (bacteria) |
Molecular weight | Theoretical: 21.932318 KDa |
Sequence | String: FTLIELMIVV AIIGILAAIA IPNFIKFQAR SKQSEAKTNL KALYTAQKSF FSEKDRYSDF ANEIGFAPER GNRYGYRVSA AAGDCEVRN AADLPVPAAG VPCISNDSFR FGANSAIDDP TPVVARFVPQ GAAGWNTTLG VQPTIADCPN CNFFAGARGN A DNEATFDD ...String: FTLIELMIVV AIIGILAAIA IPNFIKFQAR SKQSEAKTNL KALYTAQKSF FSEKDRYSDF ANEIGFAPER GNRYGYRVSA AAGDCEVRN AADLPVPAAG VPCISNDSFR FGANSAIDDP TPVVARFVPQ GAAGWNTTLG VQPTIADCPN CNFFAGARGN A DNEATFDD WVIAGFEGSG QVGPCSEAGN VASGTPYNTR NDVACDGAAQ UniProtKB: Type IV major pilin protein PilA |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | helical reconstruction |
Aggregation state | filament |
-Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 55.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Applied symmetry - Helical parameters - Δz: 10.0 Å Applied symmetry - Helical parameters - Δ&Phi: 100.7 ° Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric) Resolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 1300000 |
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Startup model | Type of model: NONE |
Final angle assignment | Type: NOT APPLICABLE / Software - Name: cryoSPARC |