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Yorodumi- PDB-6v1i: Cryo-EM reconstruction of the thermophilic bacteriophage P74-26 s... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6v1i | |||||||||
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Title | Cryo-EM reconstruction of the thermophilic bacteriophage P74-26 small terminase- symmetric | |||||||||
Components | Small terminase protein | |||||||||
Keywords | VIRAL PROTEIN / small terminase / bacteriophage / helix-turn-helix / motor | |||||||||
Function / homology | Uncharacterized protein Function and homology information | |||||||||
Biological species | Thermus virus P74-26 | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.8 Å | |||||||||
Authors | Hayes, J.A. / Hilbert, B.J. / Gaubitz, C. / Stone, N.P. / Kelch, B.A. | |||||||||
Funding support | United States, 2items
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Citation | Journal: J Biol Chem / Year: 2020 Title: A thermophilic phage uses a small terminase protein with a fixed helix-turn-helix geometry. Authors: Janelle A Hayes / Brendan J Hilbert / Christl Gaubitz / Nicholas P Stone / Brian A Kelch / Abstract: Tailed bacteriophages use a DNA-packaging motor to encapsulate their genome during viral particle assembly. The small terminase (TerS) component of this DNA-packaging machinery acts as a molecular ...Tailed bacteriophages use a DNA-packaging motor to encapsulate their genome during viral particle assembly. The small terminase (TerS) component of this DNA-packaging machinery acts as a molecular matchmaker that recognizes both the viral genome and the main motor component, the large terminase (TerL). However, how TerS binds DNA and the TerL protein remains unclear. Here we identified gp83 of the thermophilic bacteriophage P74-26 as the TerS protein. We found that TerS oligomerizes into a nonamer that binds DNA, stimulates TerL ATPase activity, and inhibits TerL nuclease activity. A cryo-EM structure of TerS revealed that it forms a ring with a wide central pore and radially arrayed helix-turn-helix domains. The structure further showed that these helix-turn-helix domains, which are thought to bind DNA by wrapping the double helix around the ring, are rigidly held in an orientation distinct from that seen in other TerS proteins. This rigid arrangement of the putative DNA-binding domain imposed strong constraints on how TerS can bind DNA. Finally, the TerS structure lacked the conserved C-terminal β-barrel domain used by other TerS proteins for binding TerL. This suggests that a well-ordered C-terminal β-barrel domain is not required for TerS to carry out its matchmaking function. Our work highlights a thermophilic system for studying the role of small terminase proteins in viral maturation and presents the structure of TerS, revealing key differences between this thermophilic phage and its mesophilic counterparts. | |||||||||
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 | 6v1i.cif.gz | 215.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6v1i.ent.gz | 176.3 KB | Display | PDB format |
PDBx/mmJSON format | 6v1i.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v1/6v1i ftp://data.pdbj.org/pub/pdb/validation_reports/v1/6v1i | HTTPS FTP |
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-Related structure data
Related structure data | 21012MC 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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-Components
#1: Protein | Mass: 19080.887 Da / Num. of mol.: 9 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus virus P74-26 / Gene: P74p83 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: A7XXR0 |
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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: Gene product 83 of the Thermus thermophilus bacteriophage P74-26 Type: COMPLEX / Entity ID: all / Source: RECOMBINANT | ||||||||||||||||||||
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Molecular weight | Value: 0.171 MDa / Experimental value: YES | ||||||||||||||||||||
Source (natural) | Organism: Thermus virus P74-26 | ||||||||||||||||||||
Source (recombinant) | Organism: Escherichia coli BL21 (bacteria) | ||||||||||||||||||||
Buffer solution | pH: 7.5 | ||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 3.4 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: This sample was monodisperse (PDI= 1.000) | ||||||||||||||||||||
Specimen support | Details: 20 mA | ||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 283 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: TFS KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Calibrated magnification: 13000 X / Calibrated defocus min: 1400 nm / Calibrated defocus max: 2600 nm / Cs: 2.7 mm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN |
Image recording | Electron dose: 50 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 2 / Num. of real images: 2822 |
-Processing
Software | Name: PHENIX / Version: 1.13_2998: / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | |||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C9 (9 fold cyclic) | |||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 84860 / Symmetry type: POINT | |||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT / Space: REAL | |||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 4XVN Pdb chain-ID: A / Accession code: 4XVN / Pdb chain residue range: 1-137 / Source name: PDB / Type: experimental model |