+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-36427 | |||||||||
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Title | Flagellar fibrils from Bacillus amyloliquefaciens | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Flagella / motor / fibril / PROTEIN FIBRIL | |||||||||
Biological species | Bacillus amyloliquefaciens (bacteria) | |||||||||
Method | helical reconstruction / cryo EM / Resolution: 2.9 Å | |||||||||
Authors | Cao Q / Cheng Y | |||||||||
Funding support | China, 1 items
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Citation | Journal: Nat Commun / Year: 2023 Title: Serine peptidase Vpr forms enzymatically active fibrils outside Bacillus bacteria revealed by cryo-EM. Authors: Yijia Cheng / Jianting Han / Meinai Song / Shuqin Zhang / Qin Cao / Abstract: Bacteria develop a variety of extracellular fibrous structures crucial for their survival, such as flagella and pili. In this study, we use cryo-EM to identify protein fibrils surrounding lab- ...Bacteria develop a variety of extracellular fibrous structures crucial for their survival, such as flagella and pili. In this study, we use cryo-EM to identify protein fibrils surrounding lab-cultured Bacillus amyloiquefaciens and discover an unreported fibril species in addition to the flagellar fibrils. These previously unknown fibrils are composed of Vpr, an extracellular serine peptidase. We find that Vpr assembles into fibrils in an enzymatically active form, potentially representing a strategy of enriching Vpr activities around bacterial cells. Vpr fibrils are also observed under other culture conditions and around other Bacillus bacteria, such as Bacillus subtilis, which may suggest a general mechanism across all Bacillus bacterial groups. Taken together, our study reveals fibrils outside the bacterial cell and sheds light on the physiological role of these extracellular fibrils. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_36427.map.gz | 110.2 MB | EMDB map data format | |
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Header (meta data) | emd-36427-v30.xml emd-36427.xml | 13 KB 13 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_36427_fsc.xml | 11.3 KB | Display | FSC data file |
Images | emd_36427.png | 85.6 KB | ||
Filedesc metadata | emd-36427.cif.gz | 4.9 KB | ||
Others | emd_36427_half_map_1.map.gz emd_36427_half_map_2.map.gz | 97.2 MB 97.2 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-36427 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-36427 | HTTPS FTP |
-Validation report
Summary document | emd_36427_validation.pdf.gz | 1 MB | Display | EMDB validaton report |
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Full document | emd_36427_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | emd_36427_validation.xml.gz | 18.8 KB | Display | |
Data in CIF | emd_36427_validation.cif.gz | 24.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-36427 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-36427 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_36427.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.05 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_36427_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_36427_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Bacillus amyloliquefaciens
Entire | Name: Bacillus amyloliquefaciens (bacteria) |
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Components |
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-Supramolecule #1: Bacillus amyloliquefaciens
Supramolecule | Name: Bacillus amyloliquefaciens / type: cell / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Bacillus amyloliquefaciens (bacteria) |
-Macromolecule #1: Flagella
Macromolecule | Name: Flagella / type: protein_or_peptide / ID: 1 / Number of copies: 33 / Enantiomer: LEVO |
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Source (natural) | Organism: Bacillus amyloliquefaciens (bacteria) |
Molecular weight | Theoretical: 35.12884 KDa |
Sequence | String: MRINHNIAAL NTSRQLNAGS NAASKNMEKL SSGLRINRAG DDAAGLAISE KMRSQIRGLD MASKNAQDGI SLIQTSEGAL NETHSILQR MSELATQAAN DTNTDSDRSE LQKEMDQLAS EVTRISTDTE FNTKKLLDGT AQNLTFQIGA NEGQTMSLSI N KMDSESLK ...String: MRINHNIAAL NTSRQLNAGS NAASKNMEKL SSGLRINRAG DDAAGLAISE KMRSQIRGLD MASKNAQDGI SLIQTSEGAL NETHSILQR MSELATQAAN DTNTDSDRSE LQKEMDQLAS EVTRISTDTE FNTKKLLDGT AQNLTFQIGA NEGQTMSLSI N KMDSESLK VGTTYTANDD GSKLVTADGK EATLVTDGSK GPNGYYDDAD KLVYQADSAL AKDTKVTKGI DISSSAKAAS SA LTTIKTA IDTVSSERAK LGAVQNRLEH TINNLGTSSE NLTSAESRIR DVDMASEMME YTKNNILTQA SQAMLAQANQ QPQ QVLQLL KG |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | helical reconstruction |
Aggregation state | cell |
-Sample preparation
Buffer | pH: 7.4 |
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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 QUANTUM (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 40.0 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: 4.6000000000000005 µm / Nominal defocus min: 0.6 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |