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- PDB-9c3b: Structure of the Shigella flexneri bacteriophage Sf14 - tail helical -
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Open data
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Basic information
Entry | Database: PDB / ID: 9c3b | |||||||||
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Title | Structure of the Shigella flexneri bacteriophage Sf14 - tail helical | |||||||||
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![]() | VIRUS / Sf14 | |||||||||
Function / homology | Structural protein ORF10, bacteriophage KPP10 / Protein of unknown function DUF3383 / Bacteriophage KPP10, Structural protein ORF10 / Protein of unknown function (DUF3383) / Uncharacterized protein / Putative structural protein![]() | |||||||||
Biological species | ![]() | |||||||||
Method | ELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.4 Å | |||||||||
![]() | Subramanian, S. / Kerns, H.R. / Braverman, S.G. / Doore, S.M. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: The structure of Shigella virus Sf14 reveals the presence of two decoration proteins and two long tail fibers. Authors: Sundharraman Subramanian / Hailey R Kerns / Samantha G Braverman / Sarah M Doore / ![]() Abstract: Bacteriophage Sf14 infects the human pathogen Shigella flexneri. A previous low-resolution structure suggested the presence of a decoration protein on its T = 9 icosahedral capsid. Here, we ...Bacteriophage Sf14 infects the human pathogen Shigella flexneri. A previous low-resolution structure suggested the presence of a decoration protein on its T = 9 icosahedral capsid. Here, we determined high-resolution structures of the Sf14 capsid and neck, along with a moderate-resolution structure of the whole Sf14 tail and baseplate. These structures indicate the capsid has not one, but two different types of decoration proteins: a trimeric β-tulip lattice that covers the entire capsid and a set of Hoc-like proteins that bind preferentially to hexamers at the quasi-3-fold axes of symmetry. The neck also contains two sets of whiskers oriented in opposite directions, and the tail has two types of long tail fibers which may bind different receptors. Based on homology and phylogenetic analysis, Sf14 may be the product of multiple horizontal gene transfer events. The structures presented here can be used to investigate further hypotheses of phage structure-function relationships and structural diversity. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 120.6 KB | Display | ![]() |
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PDB format | ![]() | 91.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.6 MB | Display | ![]() |
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Full document | ![]() | 1.6 MB | Display | |
Data in XML | ![]() | 45.6 KB | Display | |
Data in CIF | ![]() | 64.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 45164MC ![]() 9c2dC ![]() 9c39C ![]() 9c3aC M: map data used to model this data C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Components
#1: Protein | Mass: 48834.770 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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#2: Protein | Mass: 16204.168 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
Has protein modification | N |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: helical reconstruction |
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Sample preparation
Component | Name: Shigella phage Sf14 / Type: VIRUS / Entity ID: all / Source: NATURAL | |||||||||||||||
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Source (natural) | Organism: ![]() | |||||||||||||||
Details of virus | Empty: NO / Enveloped: NO / Isolate: OTHER / Type: VIRION | |||||||||||||||
Natural host | Organism: Shigella flexneri Y | |||||||||||||||
Buffer solution | pH: 7.5 | |||||||||||||||
Buffer component |
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Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | |||||||||||||||
Vitrification | Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 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 / Nominal defocus max: 3500 nm / Nominal defocus min: 500 nm |
Image recording | Electron dose: 33 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
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Processing
EM software | Name: PHENIX / Version: 1.20.1_4487: / Category: model refinement | ||||||||||||||||||||||||
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CTF correction | Type: NONE | ||||||||||||||||||||||||
Helical symmerty | Angular rotation/subunit: 25.75 ° / Axial rise/subunit: 37.062 Å / Axial symmetry: C6 | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 23422 / Symmetry type: HELICAL | ||||||||||||||||||||||||
Refine LS restraints |
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