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Yorodumi- PDB-7spu: In situ cryo-EM structure of bacteriophage Sf6 gp3:gp7:gp5 comple... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7spu | ||||||
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Title | In situ cryo-EM structure of bacteriophage Sf6 gp3:gp7:gp5 complex in conformation 1 at 3.73A resolution | ||||||
Components |
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Keywords | STRUCTURAL PROTEIN / bacteriophage / Sf6 portal / gp7 / coat protein / symmetry mismatch | ||||||
Function / homology | Function and homology information symbiont genome ejection through host cell envelope, short tail mechanism / metal ion binding Similarity search - Function | ||||||
Biological species | Shigella phage Sf6 (virus) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.73 Å | ||||||
Authors | Li, F. / Cingolani, G. / Hou, C. / Yang, R. | ||||||
Funding support | United States, 1items
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Citation | Journal: Sci Adv / Year: 2022 Title: High-resolution cryo-EM structure of the virus Sf6 genome delivery tail machine. Authors: Fenglin Li / Chun-Feng David Hou / Ruoyu Yang / Richard Whitehead / Carolyn M Teschke / Gino Cingolani / Abstract: Sf6 is a bacterial virus that infects the human pathogen Here, we describe the cryo-electron microscopy structure of the Sf6 tail machine before DNA ejection, which we determined at a 2.7-angstrom ...Sf6 is a bacterial virus that infects the human pathogen Here, we describe the cryo-electron microscopy structure of the Sf6 tail machine before DNA ejection, which we determined at a 2.7-angstrom resolution. We built de novo structures of all tail components and resolved four symmetry-mismatched interfaces. Unexpectedly, we found that the tail exists in two conformations, rotated by ~6° with respect to the capsid. The two tail conformers are identical in structure but differ solely in how the portal and head-to-tail adaptor carboxyl termini bond with the capsid at the fivefold vertex, similar to a diamond held over a five-pronged ring in two nonidentical states. Thus, in the mature Sf6 tail, the portal structure does not morph locally to accommodate the symmetry mismatch but exists in two energetic minima rotated by a discrete angle. We propose that the design principles of the Sf6 tail are conserved across P22-like Podoviridae. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7spu.cif.gz | 4.2 MB | Display | PDBx/mmCIF format |
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PDB format | pdb7spu.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7spu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7spu_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 7spu_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 7spu_validation.xml.gz | 463.7 KB | Display | |
Data in CIF | 7spu_validation.cif.gz | 736.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sp/7spu ftp://data.pdbj.org/pub/pdb/validation_reports/sp/7spu | HTTPS FTP |
-Related structure data
Related structure data | 25372MC 7sfsC 7sg7C 7sp4C 7ukjC 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: 17753.889 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Shigella phage Sf6 (virus) / References: UniProt: Q716G8 #2: Protein | Mass: 79558.227 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Shigella phage Sf6 (virus) / References: UniProt: Q716H2 #3: Protein | Mass: 45722.031 Da / Num. of mol.: 30 / Source method: isolated from a natural source / Source: (natural) Shigella phage Sf6 (virus) / References: UniProt: Q716H0 |
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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: Shigella virus Sf6 / Type: VIRUS / Entity ID: all / Source: NATURAL |
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Source (natural) | Organism: Shigella virus Sf6 |
Details of virus | Empty: YES / Enveloped: YES / Isolate: OTHER / Type: VIRION |
Buffer solution | pH: 7.5 |
Buffer component | Name: PBS |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/1 |
Vitrification | 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: TFS KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER |
Electron lens | Mode: OTHER / Nominal magnification: 81000 X / Nominal defocus max: 1500 nm / Nominal defocus min: 500 nm / Cs: 2.7 mm / C2 aperture diameter: 100 µm |
Specimen holder | Cryogen: NITROGEN |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of real images: 7977 |
-Processing
Software |
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
Particle selection | Num. of particles selected: 67439 | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.73 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 39000 / Symmetry type: POINT | ||||||||||||||||||||||||
Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||
Displacement parameters | Biso mean: 115.08 Å2 | ||||||||||||||||||||||||
Refine LS restraints |
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