+Open data
-Basic information
Entry | Database: PDB / ID: 2hi5 | ||||||
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Title | Model for bacteriophage fd from cryo-EM | ||||||
Components | Coat protein B | ||||||
Keywords | VIRUS / helix / helical VIRUS / structural protein / DNA binding protein | ||||||
Function / homology | Phage major coat protein, Gp8 / Bacteriophage M13, G8P, capsid domain superfamily / Capsid protein G8P / helical viral capsid / host cell membrane / membrane / Capsid protein G8P Function and homology information | ||||||
Biological species | Enterobacteria phage fd (virus) | ||||||
Method | ELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 8 Å | ||||||
Authors | Wang, Y.A. / Yu, X. / Overman, S. / Tsuboi, M. / Thomas, G.J. / Egelman, E.H. | ||||||
Citation | Journal: J Mol Biol / Year: 2006 Title: The structure of a filamentous bacteriophage. Authors: Ying A Wang / Xiong Yu / Stacy Overman / Masamichi Tsuboi / George J Thomas / Edward H Egelman / Abstract: Many thin helical polymers, including bacterial pili and filamentous bacteriophage, have been seen as refractory to high-resolution studies by electron microscopy. Studies of the quaternary structure ...Many thin helical polymers, including bacterial pili and filamentous bacteriophage, have been seen as refractory to high-resolution studies by electron microscopy. Studies of the quaternary structure of such filaments have depended upon techniques such as modeling or X-ray fiber diffraction, given that direct visualization of the subunit organization has not been possible. We report the first image reconstruction of a filamentous virus, bacteriophage fd, by cryoelectron microscopy. Although these thin ( approximately 70 A in diameter) rather featureless filaments scatter weakly, we have been able to achieve a nominal resolution of approximately 8 A using an iterative helical reconstruction procedure. We show that two different conformations of the virus exist, and that in both states the subunits are packed differently than in conflicting models previously proposed on the basis of X-ray fiber diffraction or solid-state NMR studies. A significant fraction of the population of wild-type fd is either disordered or in multiple conformational states, while in the presence of the Y21M mutation, this heterogeneity is greatly reduced, consistent with previous observations. These results show that new computational approaches to helical reconstruction can greatly extend the ability to visualize heterogeneous protein polymers at a reasonably high resolution. | ||||||
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 | 2hi5.cif.gz | 18.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2hi5.ent.gz | 10.5 KB | Display | PDB format |
PDBx/mmJSON format | 2hi5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hi/2hi5 ftp://data.pdbj.org/pub/pdb/validation_reports/hi/2hi5 | HTTPS FTP |
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-Related structure data
Related structure data | 1240MC 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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Symmetry | Helical symmetry: (Circular symmetry: 5 / Dyad axis: no / N subunits divisor: 1 / Num. of operations: 55 / Rise per n subunits: 17.4 Å / Rotation per n subunits: -34.616 °) |
Details | helical polymer |
-Components
#1: Protein/peptide | Mass: 5244.000 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterobacteria phage fd (virus) / Genus: Inovirus / Species: Enterobacteria phage M13 / Production host: Escherichia coli (E. coli) / References: UniProt: P69539 |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: FILAMENT / 3D reconstruction method: helical reconstruction |
-Sample preparation
Component |
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Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | |||||||||||||||
Vitrification | Cryogen name: ETHANE / Method: Blot for 2 seconds before plunging |
-Electron microscopy imaging
Experimental equipment | Model: Tecnai F20 / Image courtesy: FEI Company |
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Microscopy | Model: FEI TECNAI F20 |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 50000 X / Nominal defocus max: 3800 nm / Nominal defocus min: 1400 nm |
Specimen holder | Specimen holder type: Gatan |
Image recording | Film or detector model: KODAK SO-163 FILM |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M |
Radiation wavelength | Relative weight: 1 |
-Processing
EM software | Name: IHRSR / Category: 3D reconstruction | ||||||||||||
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CTF correction | Details: phase flipping of entire images | ||||||||||||
3D reconstruction | Method: IHRSR / Resolution: 8 Å / Resolution method: FSC 0.5 CUT-OFF / Num. of particles: 16367 / Nominal pixel size: 2.4 Å / Actual pixel size: 2.4 Å / Magnification calibration: TMV Details: The C-N bond distance is 0.09 A between GLN15 and ALA16, 0.12 A between ALA35 and THR36 and 0.44 A between ALA25 and TRP26 Symmetry type: HELICAL | ||||||||||||
Refinement step | Cycle: LAST
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