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Yorodumi- EMDB-10648: CryoEM structure of the narrow type IV pilus (PilA5) from Thermus... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-10648 | |||||||||
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Title | CryoEM structure of the narrow type IV pilus (PilA5) from Thermus thermophilus | |||||||||
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Sample |
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Function / homology | Prokaryotic N-terminal methylation site. / Prokaryotic N-terminal methylation motif / Prokaryotic N-terminal methylation site / cell outer membrane / membrane => GO:0016020 / periplasmic space / plasma membrane / Type IV narrow pilus major component PilA5 Function and homology information | |||||||||
Biological species | Thermus thermophilus HB27 (bacteria) / Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039) (bacteria) | |||||||||
Method | helical reconstruction / cryo EM / Resolution: 3.49 Å | |||||||||
Authors | Neuhaus A / Gold VAM | |||||||||
Funding support | United Kingdom, 1 items
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Citation | Journal: Nat Commun / Year: 2020 Title: Cryo-electron microscopy reveals two distinct type IV pili assembled by the same bacterium. Authors: Alexander Neuhaus / Muniyandi Selvaraj / Ralf Salzer / Julian D Langer / Kerstin Kruse / Lennart Kirchner / Kelly Sanders / Bertram Daum / Beate Averhoff / Vicki A M Gold / Abstract: Type IV pili are flexible filaments on the surface of bacteria, consisting of a helical assembly of pilin proteins. They are involved in bacterial motility (twitching), surface adhesion, biofilm ...Type IV pili are flexible filaments on the surface of bacteria, consisting of a helical assembly of pilin proteins. They are involved in bacterial motility (twitching), surface adhesion, biofilm formation and DNA uptake (natural transformation). Here, we use cryo-electron microscopy and mass spectrometry to show that the bacterium Thermus thermophilus produces two forms of type IV pilus ('wide' and 'narrow'), differing in structure and protein composition. Wide pili are composed of the major pilin PilA4, while narrow pili are composed of a so-far uncharacterized pilin which we name PilA5. Functional experiments indicate that PilA4 is required for natural transformation, while PilA5 is important for twitching motility. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_10648.map.gz | 361.9 KB | EMDB map data format | |
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Header (meta data) | emd-10648-v30.xml emd-10648.xml | 9.3 KB 9.3 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_10648_fsc.xml | 5.4 KB | Display | FSC data file |
Images | emd_10648.png | 118 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-10648 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-10648 | HTTPS FTP |
-Validation report
Summary document | emd_10648_validation.pdf.gz | 254.6 KB | Display | EMDB validaton report |
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Full document | emd_10648_full_validation.pdf.gz | 253.7 KB | Display | |
Data in XML | emd_10648_validation.xml.gz | 8.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-10648 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-10648 | HTTPS FTP |
-Related structure data
Related structure data | 6xxeMC 6xxdC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_10648.map.gz / Format: CCP4 / Size: 12.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 1.048 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Thermus thermophilus narrow pilus
Entire | Name: Thermus thermophilus narrow pilus |
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Components |
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-Supramolecule #1: Thermus thermophilus narrow pilus
Supramolecule | Name: Thermus thermophilus narrow pilus / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Thermus thermophilus HB27 (bacteria) |
-Macromolecule #1: Uncharacterized protein
Macromolecule | Name: Uncharacterized protein / type: protein_or_peptide / ID: 1 Details: Sequence corresponds to the mature protein. The first 5 residues are removed by prepilin peptidase. Number of copies: 16 / Enantiomer: LEVO |
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Source (natural) | Organism: Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039) (bacteria) |
Molecular weight | Theoretical: 11.425754 KDa |
Sequence | String: FTLIELAIVI VIIGILVAIA VPRFVDLTDQ ANQANVDATA AAVRSAYAIA TVQAKGIPTC DQVFANPEGG STSGSTWTSS DNSTTVSCN ASADTFTISR GGKTRTLNLT VN |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | helical reconstruction |
Aggregation state | filament |
-Sample preparation
Buffer | pH: 8 |
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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 K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Frames/image: 1-40 / Average electron dose: 47.6 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |