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- PDB-7dn2: Acidic stable capsid structure of Helicobacter pylori bacteriopha... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7dn2 | |||||||||
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Title | Acidic stable capsid structure of Helicobacter pylori bacteriophage KHP30 | |||||||||
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![]() | VIRUS / CAPSID / PHAGE / PHAGE HEAD / CRYOEM | |||||||||
Function / homology | Protein of unknown function DUF4043 / Protein of unknown function (DUF4043) / Major structural protein ORF14 / Uncharacterized protein![]() | |||||||||
Biological species | ![]() | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.7 Å | |||||||||
![]() | Kamiya, R. / Uchiyama, J. / Matsuzaki, S. / Murata, K. / Iwasaki, K. / Miyazaki, N. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Acid-stable capsid structure of Helicobacter pylori bacteriophage KHP30 by single-particle cryoelectron microscopy. Authors: Ryosuke Kamiya / Jumpei Uchiyama / Shigenobu Matsuzaki / Kazuyoshi Murata / Kenji Iwasaki / Naoyuki Miyazaki / ![]() Abstract: The acid-stable capsid structures of Helicobacter pylori phages KHP30 and KHP40 are solved at 2.7 and 3.0 Å resolutions by cryoelectron microscopy, respectively. The capsids have icosahedral T = 9 ...The acid-stable capsid structures of Helicobacter pylori phages KHP30 and KHP40 are solved at 2.7 and 3.0 Å resolutions by cryoelectron microscopy, respectively. The capsids have icosahedral T = 9 symmetry and consist of each 540 copies of 2 structural proteins, a major capsid protein, and a cement protein. The major capsid proteins form 12 pentagonal capsomeres occupying icosahedral vertexes and 80 hexagonal capsomeres located at icosahedral faces and edges. The major capsid protein has a unique protruding loop extending to the neighboring subunit that stabilizes hexagonal capsomeres. Furthermore, the capsid is decorated with trimeric cement proteins with a jelly roll motif. The cement protein trimer sits on the quasi-three-fold axis formed by three major capsid protein capsomeres, thereby enhancing the particle stability by connecting these capsomeres. Sequence and structure comparisons between the related Helicobacter pylori phages suggest a possible mechanism of phage adaptation to the human gastric environment. | |||||||||
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Structure visualization
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 733.4 KB | Display | ![]() |
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PDB format | ![]() | 618.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 112.9 KB | Display | |
Data in CIF | ![]() | 179.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 30778MC ![]() 7douC ![]() 7f2pC M: map data used to model this data C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Symmetry | Point symmetry: (Schoenflies symbol: I (icosahedral)) |
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Components
#1: Protein | Mass: 42465.922 Da / Num. of mol.: 9 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: I7H0H9 #2: Protein | Mass: 13721.461 Da / Num. of mol.: 9 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: I7HFW5 |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: Helicobacter phage KHP / Type: VIRUS / Entity ID: all / Source: NATURAL |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: ![]() |
Details of virus | Empty: NO / Enveloped: NO / Isolate: OTHER / Type: VIRION |
Virus shell | Name: Head / Diameter: 700 nm / Triangulation number (T number): 9 |
Buffer solution | pH: 7.2 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K |
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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: ![]() |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Average exposure time: 1 sec. / Electron dose: 20 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k) |
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Processing
Software | Name: PHENIX / Version: 1.16_3549: / Classification: refinement | ||||||||||||||||||||||||
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EM software | Name: RELION / Category: 3D reconstruction | ||||||||||||||||||||||||
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
Symmetry | Point symmetry: I (icosahedral) | ||||||||||||||||||||||||
3D reconstruction | Resolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 20737 / Algorithm: FOURIER SPACE / Symmetry type: POINT | ||||||||||||||||||||||||
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