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Yorodumi- PDB-5oh0: The Cryo-Electron Microscopy Structure of the Type 1 Chaperone-Us... -
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-Basic information
Entry | Database: PDB / ID: 5oh0 | ||||||
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Title | The Cryo-Electron Microscopy Structure of the Type 1 Chaperone-Usher Pilus Rod | ||||||
Components | Type-1 fimbrial protein, A chain | ||||||
Keywords | PROTEIN FIBRIL / bacterial pilus / chaperone-usher pilus | ||||||
Function / homology | Function and homology information cell adhesion involved in single-species biofilm formation / pilus / cell adhesion / identical protein binding Similarity search - Function | ||||||
Biological species | Escherichia coli J96 (bacteria) | ||||||
Method | ELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 4.2 Å | ||||||
Authors | Hospenthal, M.K. / Costa, T.R.D. / Redzej, A. / Waksman, G. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Structure / Year: 2017 Title: The Cryoelectron Microscopy Structure of the Type 1 Chaperone-Usher Pilus Rod. Authors: Manuela K Hospenthal / Dawid Zyla / Tiago R D Costa / Adam Redzej / Christoph Giese / James Lillington / Rudi Glockshuber / Gabriel Waksman / Abstract: Adhesive chaperone-usher pili are long, supramolecular protein fibers displayed on the surface of many bacterial pathogens. The type 1 and P pili of uropathogenic Escherichia coli (UPEC) play ...Adhesive chaperone-usher pili are long, supramolecular protein fibers displayed on the surface of many bacterial pathogens. The type 1 and P pili of uropathogenic Escherichia coli (UPEC) play important roles during urinary tract colonization, mediating attachment to the bladder and kidney, respectively. The biomechanical properties of the helical pilus rods allow them to reversibly uncoil in response to flow-induced forces, allowing UPEC to retain a foothold in the unique and hostile environment of the urinary tract. Here we provide the 4.2-Å resolution cryo-EM structure of the type 1 pilus rod, which together with the previous P pilus rod structure rationalizes the remarkable "spring-like" properties of chaperone-usher pili. The cryo-EM structure of the type 1 pilus rod differs in its helical parameters from the structure determined previously by a hybrid approach. We provide evidence that these structural differences originate from different quaternary structures of pili assembled in vivo and in vitro. | ||||||
History |
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-Structure visualization
Movie |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 5oh0.cif.gz | 144.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5oh0.ent.gz | 121.2 KB | Display | PDB format |
PDBx/mmJSON format | 5oh0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5oh0_validation.pdf.gz | 735.9 KB | Display | wwPDB validaton report |
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Full document | 5oh0_full_validation.pdf.gz | 739.3 KB | Display | |
Data in XML | 5oh0_validation.xml.gz | 29.2 KB | Display | |
Data in CIF | 5oh0_validation.cif.gz | 39.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oh/5oh0 ftp://data.pdbj.org/pub/pdb/validation_reports/oh/5oh0 | HTTPS FTP |
-Related structure data
Related structure data | 3809MC 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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1 |
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-Components
#1: Protein | Mass: 15835.243 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli J96 (bacteria) / Gene: fimA, pilA, b4314, JW4277 / Production host: Escherichia coli HB101 (bacteria) / References: UniProt: P04128 |
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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: Type 1 Chaperone-usher pilus / Type: COMPLEX Details: Superhelical assembly of the pilus rod subunit FimA Entity ID: all / Source: RECOMBINANT | ||||||||||||
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Molecular weight | Experimental value: NO | ||||||||||||
Source (natural) | Organism: Escherichia coli J96 (bacteria) | ||||||||||||
Source (recombinant) | Organism: Escherichia coli HB101 (bacteria) | ||||||||||||
Buffer solution | pH: 7.5 | ||||||||||||
Buffer component |
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Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||
Specimen support | Grid type: Quantifoil 1.2/1.3 400 mesh grid | ||||||||||||
Vitrification | Cryogen name: ETHANE / Humidity: 95 % |
-Electron microscopy imaging
Experimental equipment | Model: Tecnai Polara / Image courtesy: FEI Company |
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Microscopy | Model: FEI POLARA 300 |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 1.7 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
Software | Name: PHENIX / Version: dev_2776: / Classification: refinement | |||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | |||||||||||||||||||||||||
Helical symmerty | Angular rotation/subunit: 114.992 ° / Axial rise/subunit: 8.01188 Å / Axial symmetry: C1 | |||||||||||||||||||||||||
Particle selection | Num. of particles selected: 115545 | |||||||||||||||||||||||||
3D reconstruction | Resolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 115510 / Symmetry type: HELICAL | |||||||||||||||||||||||||
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