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Yorodumi- EMDB-29249: Structure of the Pyrobaculum calidifontis flagellar-like archaeal... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-29249 | |||||||||
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Title | Structure of the Pyrobaculum calidifontis flagellar-like archaeal type IV pilus | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Archaea / type IV pili / STRUCTURAL PROTEIN | |||||||||
Function / homology | membrane / Flagellar biosynthesis protein FlaG Function and homology information | |||||||||
Biological species | Pyrobaculum calidifontis (archaea) | |||||||||
Method | helical reconstruction / cryo EM / Resolution: 4.3 Å | |||||||||
Authors | Wang F / Kreutzberger MA / Cvirkaite-Krupovic V / Krupovic M / Egelman EH | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Proc Natl Acad Sci U S A / Year: 2023 Title: The evolution of archaeal flagellar filaments. Authors: Mark A B Kreutzberger / Virginija Cvirkaite-Krupovic / Ying Liu / Diana P Baquero / Junfeng Liu / Ravi R Sonani / Chris R Calladine / Fengbin Wang / Mart Krupovic / Edward H Egelman / Abstract: Flagellar motility has independently arisen three times during evolution: in bacteria, archaea, and eukaryotes. In prokaryotes, the supercoiled flagellar filaments are composed largely of a single ...Flagellar motility has independently arisen three times during evolution: in bacteria, archaea, and eukaryotes. In prokaryotes, the supercoiled flagellar filaments are composed largely of a single protein, bacterial or archaeal flagellin, although these two proteins are not homologous, while in eukaryotes, the flagellum contains hundreds of proteins. Archaeal flagellin and archaeal type IV pilin are homologous, but how archaeal flagellar filaments (AFFs) and archaeal type IV pili (AT4Ps) diverged is not understood, in part, due to the paucity of structures for AFFs and AT4Ps. Despite having similar structures, AFFs supercoil, while AT4Ps do not, and supercoiling is essential for the function of AFFs. We used cryo-electron microscopy to determine the atomic structure of two additional AT4Ps and reanalyzed previous structures. We find that all AFFs have a prominent 10-strand packing, while AT4Ps show a striking structural diversity in their subunit packing. A clear distinction between all AFF and all AT4P structures involves the extension of the N-terminal α-helix with polar residues in the AFFs. Additionally, we characterize a flagellar-like AT4P from with filament and subunit structure similar to that of AFFs which can be viewed as an evolutionary link, showing how the structural diversity of AT4Ps likely allowed for an AT4P to evolve into a supercoiling AFF. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_29249.map.gz | 7.8 MB | EMDB map data format | |
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Header (meta data) | emd-29249-v30.xml emd-29249.xml | 13.3 KB 13.3 KB | Display Display | EMDB header |
Images | emd_29249.png | 71.5 KB | ||
Masks | emd_29249_msk_1.map | 125 MB | Mask map | |
Others | emd_29249_half_map_1.map.gz emd_29249_half_map_2.map.gz | 116.1 MB 116.1 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-29249 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-29249 | HTTPS FTP |
-Validation report
Summary document | emd_29249_validation.pdf.gz | 1.1 MB | Display | EMDB validaton report |
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Full document | emd_29249_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | emd_29249_validation.xml.gz | 14 KB | Display | |
Data in CIF | emd_29249_validation.cif.gz | 16.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-29249 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-29249 | HTTPS FTP |
-Related structure data
Related structure data | 8fk7MC 7txiC 8fj5C 8fjsC 8fk0C 8gi2C 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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-Map
File | Download / File: emd_29249.map.gz / Format: CCP4 / Size: 125 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
-Mask #1
File | emd_29249_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_29249_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_29249_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Archaeal type IV pilus
Entire | Name: Archaeal type IV pilus |
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Components |
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-Supramolecule #1: Archaeal type IV pilus
Supramolecule | Name: Archaeal type IV pilus / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Pyrobaculum calidifontis (archaea) |
-Macromolecule #1: Flagellin
Macromolecule | Name: Flagellin / type: protein_or_peptide / ID: 1 / Number of copies: 20 / Enantiomer: LEVO |
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Source (natural) | Organism: Pyrobaculum calidifontis (archaea) |
Molecular weight | Theoretical: 14.957439 KDa |
Sequence | String: MPMKTKGLEP IVAAVLLIVV AVIGAVLVYL WFSGYVTRAT SQAEQLSAAE QLKIEAVSKT GTTVSVNVRN VGEVPVKIAS AYVLNATTL TMICGGSLTS PQQIDPGTIQ TINVPGTCNL IAGARYIVKV VTARGTEAAA TFISP UniProtKB: Flagellar biosynthesis protein FlaG |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | helical reconstruction |
Aggregation state | filament |
-Sample preparation
Buffer | pH: 6 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | TFS KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 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 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Applied symmetry - Helical parameters - Δz: 4.87 Å Applied symmetry - Helical parameters - Δ&Phi: 108.92 ° Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric) Resolution.type: BY AUTHOR / Resolution: 4.3 Å / Resolution method: FSC 0.5 CUT-OFF / Number images used: 108016 |
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Startup model | Type of model: OTHER |
Final angle assignment | Type: NOT APPLICABLE |