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Open data
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Basic information
Entry | Database: PDB / ID: 7sqt | |||||||||||||||
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Title | Goslar chimallin cubic (O, 24mer) assembly | |||||||||||||||
![]() | Chimallin | |||||||||||||||
![]() | STRUCTURAL PROTEIN / phage / viral protein | |||||||||||||||
Function / homology | host cell cytoplasm / Chimallin![]() | |||||||||||||||
Biological species | ![]() | |||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4 Å | |||||||||||||||
![]() | Laughlin, T.G. / Deep, A. / Prichard, A.M. / Seitz, C. / Gu, Y. / Enustun, E. / Suslov, S. / Khanna, K. / Birkholz, E.A. / Amaro, R.E. ...Laughlin, T.G. / Deep, A. / Prichard, A.M. / Seitz, C. / Gu, Y. / Enustun, E. / Suslov, S. / Khanna, K. / Birkholz, E.A. / Amaro, R.E. / Pogliano, J. / Corbett, K.D. / Villa, E. | |||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Architecture and self-assembly of the jumbo bacteriophage nuclear shell. Authors: Thomas G Laughlin / Amar Deep / Amy M Prichard / Christian Seitz / Yajie Gu / Eray Enustun / Sergey Suslov / Kanika Khanna / Erica A Birkholz / Emily Armbruster / J Andrew McCammon / Rommie ...Authors: Thomas G Laughlin / Amar Deep / Amy M Prichard / Christian Seitz / Yajie Gu / Eray Enustun / Sergey Suslov / Kanika Khanna / Erica A Birkholz / Emily Armbruster / J Andrew McCammon / Rommie E Amaro / Joe Pogliano / Kevin D Corbett / Elizabeth Villa / ![]() Abstract: Bacteria encode myriad defences that target the genomes of infecting bacteriophage, including restriction-modification and CRISPR-Cas systems. In response, one family of large bacteriophages uses a ...Bacteria encode myriad defences that target the genomes of infecting bacteriophage, including restriction-modification and CRISPR-Cas systems. In response, one family of large bacteriophages uses a nucleus-like compartment to protect its replicating genomes by excluding host defence factors. However, the principal composition and structure of this compartment remain unknown. Here we find that the bacteriophage nuclear shell assembles primarily from one protein, which we name chimallin (ChmA). Combining cryo-electron tomography of nuclear shells in bacteriophage-infected cells and cryo-electron microscopy of a minimal chimallin compartment in vitro, we show that chimallin self-assembles as a flexible sheet into closed micrometre-scale compartments. The architecture and assembly dynamics of the chimallin shell suggest mechanisms for its nucleation and growth, and its role as a scaffold for phage-encoded factors mediating macromolecular transport, cytoskeletal interactions, and viral maturation. | |||||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 2.2 MB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 25394MC ![]() 7sqqC ![]() 7sqrC ![]() 7sqsC ![]() 7squC ![]() 7sqvC C: citing same article ( M: map data used to model this data |
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Similar structure data | Similarity search - Function & homology ![]() |
EM raw data | ![]() Data #1: Unaligned frames as unormalized LZW-TIFF [micrographs - multiframe]) |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Components
#1: Protein | Mass: 69889.445 Da / Num. of mol.: 24 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: Goslar_00189 / Production host: ![]() ![]() |
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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 |
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Sample preparation
Component | Name: Goslar chimallin cubic (24mer) assembly / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: ![]() |
Source (recombinant) | Organism: ![]() ![]() |
Buffer solution | pH: 7.5 |
Specimen | Conc.: 2.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Details: 20 mA / Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/2 |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE-PROPANE / Humidity: 100 % / Chamber temperature: 289 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 / Cs: 2.7 mm / C2 aperture diameter: 70 µm / Alignment procedure: ZEMLIN TABLEAU |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 40 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 3921 |
EM imaging optics | Energyfilter name: GIF Quantum LS / Energyfilter slit width: 20 eV |
Image scans | Movie frames/image: 44 / Used frames/image: 1-44 |
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Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
Particle selection | Num. of particles selected: 289387 | ||||||||||||||||||||||||
Symmetry | Point symmetry: O (octahedral) | ||||||||||||||||||||||||
3D reconstruction | Resolution: 4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 78532 / Algorithm: FOURIER SPACE / Symmetry type: POINT | ||||||||||||||||||||||||
Atomic model building | B value: 319 / Protocol: AB INITIO MODEL / Space: REAL |