+Open data
-Basic information
Entry | Database: PDB / ID: 8jmv | ||||||
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Title | Flagellar fibrils from Bacillus amyloliquefaciens | ||||||
Components | Flagella | ||||||
Keywords | PROTEIN FIBRIL / Flagella / motor / fibril | ||||||
Biological species | Bacillus amyloliquefaciens (bacteria) | ||||||
Method | ELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 2.9 Å | ||||||
Authors | Cao, Q. / Cheng, Y. | ||||||
Funding support | China, 1items
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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
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8jmv.cif.gz | 1.8 MB | Display | PDBx/mmCIF format |
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PDB format | pdb8jmv.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 8jmv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8jmv_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 8jmv_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 8jmv_validation.xml.gz | 268.1 KB | Display | |
Data in CIF | 8jmv_validation.cif.gz | 362.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jm/8jmv ftp://data.pdbj.org/pub/pdb/validation_reports/jm/8jmv | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 35128.840 Da / Num. of mol.: 33 / Source method: isolated from a natural source / Source: (natural) Bacillus amyloliquefaciens (bacteria) |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: CELL / 3D reconstruction method: helical reconstruction |
-Sample preparation
Component | Name: Bacillus amyloliquefaciens / Type: CELL / Entity ID: all / Source: NATURAL |
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Source (natural) | Organism: Bacillus amyloliquefaciens (bacteria) |
Buffer solution | pH: 7.4 |
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: 4600 nm / Nominal defocus min: 600 nm |
Image recording | Electron dose: 40 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 QUANTUM (4k x 4k) |
-Processing
CTF correction | Type: NONE |
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Helical symmerty | Angular rotation/subunit: 65.4 ° / Axial rise/subunit: 4.77 Å / Axial symmetry: C1 |
3D reconstruction | Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 153285 / Symmetry type: HELICAL |