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Yorodumi- PDB-6a7f: The cryo-EM structure of filamentous bacteriophage IKe major coat... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6a7f | ||||||||||||
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Title | The cryo-EM structure of filamentous bacteriophage IKe major coat protein p8 shell assembly. | ||||||||||||
Components | major coat protein p8 | ||||||||||||
Keywords | VIRAL PROTEIN / filamentous bacteriophage / major coat protein | ||||||||||||
Function / homology | Function and homology information | ||||||||||||
Biological species | Filamentous phage (virus) | ||||||||||||
Method | ELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.4 Å | ||||||||||||
Authors | Xu, J.W. / Dayan, N. / Goldbourt, A. / Xiang, Y. | ||||||||||||
Funding support | China, 3items
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Citation | Journal: Proc Natl Acad Sci U S A / Year: 2019 Title: Cryo-electron microscopy structure of the filamentous bacteriophage IKe. Authors: Jingwei Xu / Nir Dayan / Amir Goldbourt / Ye Xiang / Abstract: The filamentous bacteriophage IKe infects cells bearing IncN pili. We report the cryo-electron microscopy structure of the micrometer-long IKe viral particle at a resolution of 3.4 Å. The major ...The filamentous bacteriophage IKe infects cells bearing IncN pili. We report the cryo-electron microscopy structure of the micrometer-long IKe viral particle at a resolution of 3.4 Å. The major coat protein [protein 8 (p8)] consists of 47 residues that fold into a ∼68-Å-long helix. An atomic model of the coat protein was built. Five p8 helices in a horizontal layer form a pentamer, and symmetrically neighboring p8 layers form a right-handed helical cylinder having a rise per pentamer of 16.77 Å and a twist of 38.52°. The inner surface of the capsid cylinder is positively charged and has direct interactions with the encapsulated circular single-stranded DNA genome, which has an electron density consistent with an unusual left-handed helix structure. Similar to capsid structures of other filamentous viruses, strong capsid packing in the IKe particle is maintained by hydrophobic residues. Despite having a different length and large sequence differences from other filamentous phages, π-π interactions were found between Tyr9 of one p8 and Trp29 of a neighboring p8 in IKe that are similar to interactions observed in phage M13, suggesting that, despite sequence divergence, overall structural features are maintained. | ||||||||||||
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 | 6a7f.cif.gz | 230.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6a7f.ent.gz | 193.5 KB | Display | PDB format |
PDBx/mmJSON format | 6a7f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6a7f_validation.pdf.gz | 675.2 KB | Display | wwPDB validaton report |
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Full document | 6a7f_full_validation.pdf.gz | 674.5 KB | Display | |
Data in XML | 6a7f_validation.xml.gz | 28 KB | Display | |
Data in CIF | 6a7f_validation.cif.gz | 48.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a7/6a7f ftp://data.pdbj.org/pub/pdb/validation_reports/a7/6a7f | HTTPS FTP |
-Related structure data
Related structure data | 6993MC 6994C 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: 5700.578 Da / Num. of mol.: 30 / Source method: isolated from a natural source / Source: (natural) Filamentous phage (virus) / Strain: IKe / References: UniProt: P03620 |
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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 | Name: Filamentous phage / Type: VIRUS / Entity ID: all / Source: NATURAL |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: Filamentous phage (virus) / Strain: IKe |
Details of virus | Empty: NO / Enveloped: NO / Isolate: SPECIES / Type: VIRION |
Natural host | Organism: Escherichia coli / Strain: A527 |
Virus shell | Diameter: 64 nm |
Buffer solution | pH: 7.5 / Details: 50mM Tris at pH 7.5, 10mM MgCl2, 100mM NaCl |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R1.2/1.3 |
Vitrification | Instrument: FEI VITROBOT MARK IV / 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 / Cs: 2.7 mm |
Image recording | Electron dose: 40 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||
Helical symmerty | Angular rotation/subunit: 38.52 ° / Axial rise/subunit: 16.77 Å / Axial symmetry: C5 | ||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 112808 / Symmetry type: HELICAL | ||||||||||||||||||||||||||||
Atomic model building | Protocol: AB INITIO MODEL / Space: REAL |