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Yorodumi- PDB-7a02: Bacillus endospore appendages form a novel family of disulfide-li... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7a02 | ||||||
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Title | Bacillus endospore appendages form a novel family of disulfide-linked pili | ||||||
Components | DUF3992 domain-containing protein | ||||||
Keywords | UNKNOWN FUNCTION / Pilli / Endospore / Gram-Positive / Helical reconstruction / Disulphide bridge | ||||||
Function / homology | Endospore appendages core / Endospore appendages / DUF3992 domain-containing protein Function and homology information | ||||||
Biological species | Bacillus cereus (bacteria) | ||||||
Method | ELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3 Å | ||||||
Authors | Pradhan, B. / Liedtke, J. / Sleutel, M. / Lindback, T. / Llarena, A.K. / Brynildsrud, O. / Aspholm, M. / Remaut, H. | ||||||
Funding support | Belgium, 1items
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Citation | Journal: EMBO J / Year: 2021 Title: Endospore Appendages: a novel pilus superfamily from the endospores of pathogenic Bacilli. Authors: Brajabandhu Pradhan / Janine Liedtke / Mike Sleutel / Toril Lindbäck / Ephrem Debebe Zegeye / Kristin O Sullivan / Ann-Katrin Llarena / Ola Brynildsrud / Marina Aspholm / Han Remaut / Abstract: Bacillus cereus sensu lato is a group of Gram-positive endospore-forming bacteria with high ecological diversity. Their endospores are decorated with micrometer-long appendages of unknown identity ...Bacillus cereus sensu lato is a group of Gram-positive endospore-forming bacteria with high ecological diversity. Their endospores are decorated with micrometer-long appendages of unknown identity and function. Here, we isolate endospore appendages (Enas) from the food poisoning outbreak strain B. cereus NVH 0075-95 and find proteinaceous fibers of two main morphologies: S- and L-Ena. By using cryoEM and 3D helical reconstruction of S-Enas, we show these to represent a novel class of Gram-positive pili. S-Enas consist of single domain subunits with jellyroll topology that are laterally stacked by β-sheet augmentation. S-Enas are longitudinally stabilized by disulfide bonding through N-terminal connector peptides that bridge the helical turns. Together, this results in flexible pili that are highly resistant to heat, drought, and chemical damage. Phylogenomic analysis reveals a ubiquitous presence of the ena-gene cluster in the B. cereus group, which include species of clinical, environmental, and food importance. We propose Enas to represent a new class of pili specifically adapted to the harsh conditions encountered by bacterial spores. #1: Journal: Biorxiv / Year: 2020 Title: Bacillus endospore appendages form a novel family of disulfide-linked pili Authors: Pradhan, B. / Liedtke, J. / Sleutel, M. / Lindback, T. / Llarena, A.K. / Brynildsrud, O. / Aspholm, M. / Remaut, H. | ||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 7a02.cif.gz | 400.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7a02.ent.gz | 342.5 KB | Display | PDB format |
PDBx/mmJSON format | 7a02.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7a02_validation.pdf.gz | 945.3 KB | Display | wwPDB validaton report |
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Full document | 7a02_full_validation.pdf.gz | 967.1 KB | Display | |
Data in XML | 7a02_validation.xml.gz | 53.1 KB | Display | |
Data in CIF | 7a02_validation.cif.gz | 86.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a0/7a02 ftp://data.pdbj.org/pub/pdb/validation_reports/a0/7a02 | HTTPS FTP |
-Related structure data
Related structure data | 11591MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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-Components
#1: Protein | Mass: 12162.675 Da / Num. of mol.: 23 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus cereus (bacteria) Gene: B1995_14460, B2J90_04405, BACERE00183_02460, CNQ78_18995 Plasmid: pET28a / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1Y6A695 |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: HELICAL ARRAY / 3D reconstruction method: helical reconstruction |
-Sample preparation
Component | Name: Ena1B / Type: ORGANELLE OR CELLULAR COMPONENT Details: In vitro assembled Bacillus endospore appendage comprising the subunit Ena1B Entity ID: all / Source: RECOMBINANT |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: Bacillus cereus (bacteria) / Strain: NVH 0075-95 / Organelle: endospore appendage |
Source (recombinant) | Organism: Escherichia coli (E. coli) / Plasmid: pET28a |
Buffer solution | pH: 7 |
Buffer component | Formula: H2O |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: COPPER / Grid type: Quantifoil R2/1 |
Vitrification | Instrument: GATAN CRYOPLUNGE 3 / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 298.15 K |
-Electron microscopy imaging
Microscopy | Model: JEOL CRYO ARM 300 |
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Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN |
Electron lens | Mode: BRIGHT FIELD / Calibrated magnification: 60000 X / Calibrated defocus min: 500 nm / Calibrated defocus max: 3500 nm / Alignment procedure: BASIC |
Specimen holder | Specimen holder model: JEOL 3200FSC CRYOHOLDER |
Image recording | Electron dose: 64.66 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 3000 |
-Processing
Software | Name: PHENIX / Version: 1.18.2_3874: / Classification: refinement | ||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING ONLY | ||||||||||||||||||||||||
Helical symmerty | Angular rotation/subunit: 3.43721 ° / Axial rise/subunit: 32.3504 Å / Axial symmetry: C1 | ||||||||||||||||||||||||
Particle selection | Num. of particles selected: 100495 | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 65466 / Symmetry type: HELICAL | ||||||||||||||||||||||||
Atomic model building | B value: 27.4 / Protocol: AB INITIO MODEL / Space: REAL | ||||||||||||||||||||||||
Refine LS restraints |
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