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Yorodumi- PDB-7dou: Trimeric cement protein structure of Helicobacter pylori bacterio... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7dou | |||||||||
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Title | Trimeric cement protein structure of Helicobacter pylori bacteriophage KHP40 | |||||||||
Components | Cement protein gp16 | |||||||||
Keywords | VIRUS / CAPSID / PHAGE / PHAGE HEAD / CRYOEM | |||||||||
Function / homology | Uncharacterized protein Function and homology information | |||||||||
Biological species | Helicobacter phage KHP40 (virus) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3 Å | |||||||||
Authors | Kamiya, R. / Uchiyama, J. / Matsuzaki, S. / Murata, K. / Iwasaki, K. / Miyazaki, N. | |||||||||
Funding support | Japan, 2items
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Citation | Journal: Structure / Year: 2022 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. | |||||||||
History |
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-Structure visualization
Movie |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 7dou.cif.gz | 71.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7dou.ent.gz | 54.3 KB | Display | PDB format |
PDBx/mmJSON format | 7dou.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7dou_validation.pdf.gz | 968.7 KB | Display | wwPDB validaton report |
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Full document | 7dou_full_validation.pdf.gz | 971.4 KB | Display | |
Data in XML | 7dou_validation.xml.gz | 30.1 KB | Display | |
Data in CIF | 7dou_validation.cif.gz | 43.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/do/7dou ftp://data.pdbj.org/pub/pdb/validation_reports/do/7dou | HTTPS FTP |
-Related structure data
Related structure data | 30800MC 7dn2C 7f2pC C: citing same article (ref.) M: map data used to model this data |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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-Components
#1: Protein | Mass: 13469.469 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Helicobacter phage KHP40 (virus) / References: UniProt: I7GUT5 |
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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 |
-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: Helicobacter phage KHP (virus) |
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 |
-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 |
Image recording | Average exposure time: 1 sec. / Electron dose: 20 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.18.2_3874: / 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: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 6772 / Symmetry type: POINT | ||||||||||||||||||||||||
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