8FNE

phiPA3 PhuN Tetramer, p2


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.90 Å
  • Aggregation State: 2D ARRAY 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: in silico
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

The phi PA3 phage nucleus is enclosed by a self-assembling 2D crystalline lattice.

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.

(2023) Nat Commun 14: 927-927

  • DOI: https://doi.org/10.1038/s41467-023-36526-9
  • Primary Citation of Related Structures:  
    8FNE, 8FV5

  • PubMed 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 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.


  • Organizational Affiliation

    Department of Biochemistry, University of California San Francisco, San Francisco, CA, 94143, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Maltose/maltodextrin-binding periplasmic protein, PhuN
A, B, C, D, E
A, B, C, D, E, F, G, H
996Escherichia coli K-12Pseudomonas phage PhiPA3
This entity is chimeric
Mutation(s): 0 
Gene Names: malEb4034JW3994053
UniProt
Find proteins for P0AEX9 (Escherichia coli (strain K12))
Explore P0AEX9 
Go to UniProtKB:  P0AEX9
Find proteins for F8SJT5 (Pseudomonas phage PhiPA3)
Explore F8SJT5 
Go to UniProtKB:  F8SJT5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsF8SJT5P0AEX9
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.90 Å
  • Aggregation State: 2D ARRAY 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTRosetta
MODEL REFINEMENTISOLDE1.2.1

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Department of Health & Human Services (HHS)United StatesR35GM118099
Howard Hughes Medical Institute (HHMI)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2023-03-01
    Type: Initial release
  • Version 1.1: 2024-06-19
    Changes: Data collection