+Open data
-Basic information
Entry | Database: PDB / ID: 8fv5 | |||||||||
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Title | Representation of 16-mer phiPA3 PhuN Lattice, p2 | |||||||||
Components | Maltose/maltodextrin-binding periplasmic protein, phiPA3 PhuN | |||||||||
Keywords | VIRAL PROTEIN / phiPA3 protein / shell protein / PhuN / phage nucleus | |||||||||
Function / homology | Function and homology information detection of maltose stimulus / maltose transport complex / maltose binding / maltose transport / maltodextrin transmembrane transport / carbohydrate transport / carbohydrate transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / ATP-binding cassette (ABC) transporter complex / cell chemotaxis ...detection of maltose stimulus / maltose transport complex / maltose binding / maltose transport / maltodextrin transmembrane transport / carbohydrate transport / carbohydrate transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / ATP-binding cassette (ABC) transporter complex / cell chemotaxis / outer membrane-bounded periplasmic space / host cell cytoplasm / periplasmic space / DNA damage response / membrane Similarity search - Function | |||||||||
Biological species | Escherichia coli (E. coli) Pseudomonas phage PhiPA3 (virus) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.21 Å | |||||||||
Authors | Nieweglowska, E.S. / Brilot, A.F. / Mendez-Moran, M. / Kokontis, C. / Baek, M. / Li, J. / Cheng, Y. / Baker, D. / Bondy-Denomy, J. / Agard, D.A. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Nat Commun / Year: 2023 Title: The ϕPA3 phage nucleus is enclosed by a self-assembling 2D crystalline lattice. Authors: Eliza S Nieweglowska / Axel F Brilot / Melissa Méndez-Moran / Claire Kokontis / Minkyung Baek / Junrui Li / Yifan Cheng / David Baker / Joseph Bondy-Denomy / David A Agard / Abstract: To protect themselves from host attack, numerous jumbo bacteriophages establish a phage nucleus-a micron-scale, proteinaceous structure encompassing the replicating phage DNA. Bacteriophage and host ...To protect themselves from host attack, numerous jumbo bacteriophages establish a phage nucleus-a micron-scale, proteinaceous structure encompassing the replicating phage DNA. Bacteriophage and host proteins associated with replication and transcription are concentrated inside the phage nucleus while other phage and host proteins are excluded, including CRISPR-Cas and restriction endonuclease host defense systems. Here, we show that nucleus fragments isolated from ϕPA3 infected Pseudomonas aeruginosa form a 2-dimensional lattice, having p2 or p4 symmetry. We further demonstrate that recombinantly purified primary Phage Nuclear Enclosure (PhuN) protein spontaneously assembles into similar 2D sheets with p2 and p4 symmetry. We resolve the dominant p2 symmetric state to 3.9 Å by cryo-EM. Our structure reveals a two-domain core, organized into quasi-symmetric tetramers. Flexible loops and termini mediate adaptable inter-tetramer contacts that drive subunit assembly into a lattice and enable the adoption of different symmetric states. While the interfaces between subunits are mostly well packed, two are open, forming channels that likely have functional implications for the transport of proteins, mRNA, and small molecules. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8fv5.cif.gz | 3.1 MB | Display | PDBx/mmCIF format |
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PDB format | pdb8fv5.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 8fv5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fv/8fv5 ftp://data.pdbj.org/pub/pdb/validation_reports/fv/8fv5 | HTTPS FTP |
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-Related structure data
Related structure data | 29451MC 8fneC C: citing same article (ref.) M: map data used to model this data |
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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: 110126.078 Da / Num. of mol.: 32 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (strain K12) (bacteria), (gene. exp.) Pseudomonas phage PhiPA3 (virus) Strain: K12 / Gene: malE, 053 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Star (DE3) pLysS / References: UniProt: P0AEX9, UniProt: F8SJT5 |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: 2D ARRAY / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Lattice of phiPA3 PhuN Tetramer, p2 / Type: COMPLEX / Entity ID: all / Source: MULTIPLE SOURCES | ||||||||||||||||||||||||||||
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Molecular weight | Experimental value: NO | ||||||||||||||||||||||||||||
Source (natural) | Organism: Pseudomonas phage PhiPA3 (virus) | ||||||||||||||||||||||||||||
Source (recombinant) | Organism: Escherichia coli (E. coli) / Strain: BL21 Star (DE3) pLysS | ||||||||||||||||||||||||||||
Buffer solution | pH: 6.5 Details: 0.25 cOmplete Protease Inhibitor Tablet also included | ||||||||||||||||||||||||||||
Buffer component |
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Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 283.15 K |
-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: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 105000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 67 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
-Processing
Software | Name: UCSF ChimeraX / Version: 1.5/v9 / Classification: model building / URL: https://www.rbvi.ucsf.edu/chimerax/ / Os: macOS / Type: package | |||||||||||||||||||||||||||||||||||||||||||||
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EM software |
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CTF correction | Type: NONE | |||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C2 (2 fold cyclic) | |||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 4.21 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 161270 / Symmetry type: POINT | |||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT |