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Yorodumi- PDB-8gtc: Cryo-EM model of the marine siphophage vB_DshS-R4C baseplate-tail... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8gtc | ||||||
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Title | Cryo-EM model of the marine siphophage vB_DshS-R4C baseplate-tail complex | ||||||
Components |
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Keywords | VIRAL PROTEIN / Marine bacteriophage / Cryo-EM / Siphophage / Baseplate / Megatron protein / Tail fibre protein / Distal tail protein / Hub protein | ||||||
Function / homology | Function and homology information Protein of unknown function DUF2793 / Protein of unknown function (DUF2793) / Bacteriophage phiJL001, Gp84, N-terminal / GTA TIM-barrel-like domain / Uncharacterized conserved protein (DUF2163) / GTA TIM-barrel-like domain / Protein of unknown function DUF2460 / Conserved hypothetical protein 2217 (DUF2460) / Bacteriophage phiJL001, Gp84 / Bacteriophage phiJL001, Gp84, C-terminal ...Protein of unknown function DUF2793 / Protein of unknown function (DUF2793) / Bacteriophage phiJL001, Gp84, N-terminal / GTA TIM-barrel-like domain / Uncharacterized conserved protein (DUF2163) / GTA TIM-barrel-like domain / Protein of unknown function DUF2460 / Conserved hypothetical protein 2217 (DUF2460) / Bacteriophage phiJL001, Gp84 / Bacteriophage phiJL001, Gp84, C-terminal / Phage conserved hypothetical protein BR0599 / Tip attachment protein J / Putative phage tail protein / Glycoside hydrolase superfamily Similarity search - Domain/homology | ||||||
Biological species | Dinoroseobacter phage vB_DshS-R4C (virus) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.5 Å | ||||||
Authors | Huang, Y. / Sun, H. / Wei, S. / Zheng, Q. / Li, S. / Zhang, R. / Xia, N. | ||||||
Funding support | 1items
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Citation | Journal: Nat Commun / Year: 2023 Title: Structure and proposed DNA delivery mechanism of a marine roseophage. Authors: Yang Huang / Hui Sun / Shuzhen Wei / Lanlan Cai / Liqin Liu / Yanan Jiang / Jiabao Xin / Zhenqin Chen / Yuqiong Que / Zhibo Kong / Tingting Li / Hai Yu / Jun Zhang / Ying Gu / Qingbing Zheng ...Authors: Yang Huang / Hui Sun / Shuzhen Wei / Lanlan Cai / Liqin Liu / Yanan Jiang / Jiabao Xin / Zhenqin Chen / Yuqiong Que / Zhibo Kong / Tingting Li / Hai Yu / Jun Zhang / Ying Gu / Qingbing Zheng / Shaowei Li / Rui Zhang / Ningshao Xia / Abstract: Tailed bacteriophages (order, Caudovirales) account for the majority of all phages. However, the long flexible tail of siphophages hinders comprehensive investigation of the mechanism of viral gene ...Tailed bacteriophages (order, Caudovirales) account for the majority of all phages. However, the long flexible tail of siphophages hinders comprehensive investigation of the mechanism of viral gene delivery. Here, we report the atomic capsid and in-situ structures of the tail machine of the marine siphophage, vB_DshS-R4C (R4C), which infects Roseobacter. The R4C virion, comprising 12 distinct structural protein components, has a unique five-fold vertex of the icosahedral capsid that allows genome delivery. The specific position and interaction pattern of the tail tube proteins determine the atypical long rigid tail of R4C, and further provide negative charge distribution within the tail tube. A ratchet mechanism assists in DNA transmission, which is initiated by an absorption device that structurally resembles the phage-like particle, RcGTA. Overall, these results provide in-depth knowledge into the intact structure and underlining DNA delivery mechanism for the ecologically important siphophages. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8gtc.cif.gz | 1 MB | Display | PDBx/mmCIF format |
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PDB format | pdb8gtc.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 8gtc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8gtc_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 8gtc_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 8gtc_validation.xml.gz | 166.5 KB | Display | |
Data in CIF | 8gtc_validation.cif.gz | 291.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gt/8gtc ftp://data.pdbj.org/pub/pdb/validation_reports/gt/8gtc | HTTPS FTP |
-Related structure data
Related structure data | 34249MC 8gtaC 8gtbC 8gtdC 8gtfC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 13574.816 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Dinoroseobacter phage vB_DshS-R4C (virus) / References: UniProt: A0A4Y6EGR9 #2: Protein | Mass: 23378.309 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Dinoroseobacter phage vB_DshS-R4C (virus) / References: UniProt: A0A4Y6E7X5 #3: Protein | Mass: 154569.125 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Dinoroseobacter phage vB_DshS-R4C (virus) / References: UniProt: A0A4Y6E933 #4: Protein | Mass: 31055.357 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Dinoroseobacter phage vB_DshS-R4C (virus) / References: UniProt: A0A4Y6E762 #5: Protein | Mass: 22783.799 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Source: (natural) Dinoroseobacter phage vB_DshS-R4C (virus) / References: UniProt: A0A4Y6E764 |
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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: Dinoroseobacter phage vB_DshS-R4C / Type: VIRUS / Entity ID: all / Source: NATURAL |
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Source (natural) | Organism: Dinoroseobacter phage vB_DshS-R4C (virus) |
Details of virus | Empty: NO / Enveloped: NO / Isolate: SPECIES / Type: VIRION |
Natural host | Organism: Dinoroseobacter shibae DFL 12 = DSM 16493 |
Buffer solution | pH: 7.6 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Tecnai F30 / Image courtesy: FEI Company |
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Microscopy | Model: FEI TECNAI F30 |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2200 nm / Nominal defocus min: 1000 nm |
Image recording | Electron dose: 30 e/Å2 / Film or detector model: FEI FALCON III (4k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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Symmetry | Point symmetry: C3 (3 fold cyclic) |
3D reconstruction | Resolution: 4.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 11598 / Symmetry type: POINT |