7SQR | pdb_00007sqr

201phi2-1 Chimallin localized tetramer reconstruction

• PDB DOI: https://doi.org/10.2210/pdb7SQR/pdb
• EM Map EMD-25391: EMDB EMDataResource

• Classification: STRUCTURAL PROTEIN
• Organism(s): Pseudomonas phage 201phi2-1
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2021-11-06 Released: 2022-07-27 
• Deposition Author(s): 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 Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), National Science Foundation (NSF, United States), Howard Hughes Medical Institute (HHMI)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.40 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Architecture and self-assembly of the jumbo bacteriophage nuclear shell.

Laughlin, T.G., Deep, A., Prichard, A.M., Seitz, C., Gu, Y., Enustun, E., Suslov, S., Khanna, K., Birkholz, E.A., Armbruster, E., McCammon, J.A., Amaro, R.E., Pogliano, J., Corbett, K.D., Villa, E.

(2022) Nature 608: 429-435

• PubMed: 35922510 
• DOI: https://doi.org/10.1038/s41586-022-05013-4
• Primary Citation Related Structures: 
  7SQQ, 7SQR, 7SQS, 7SQT, 7SQU, 7SQV


• PubMed Abstract: 
  

  Bacteria encode myriad defences that target the genomes of infecting bacteriophage, including restriction-modification and CRISPR-Cas systems ¹ . In response, one family of large bacteriophages uses a nucleus-like compartment to protect its replicating genomes by excluding host defence factors ^2-4 . 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.

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Organizational Affiliation: 
• Department of Molecular Biology, School of Biological Sciences, University of California San Diego, La Jolla, CA, USA.
Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA.
Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, USA.
Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA.
Department of Pharmacology, University of California San Diego, La Jolla, CA, USA.
Department of Molecular Biology, School of Biological Sciences, University of California San Diego, La Jolla, CA, USA. [e-mail].
Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA. [e-mail].
Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, USA. [e-mail].
Department of Molecular Biology, School of Biological Sciences, University of California San Diego, La Jolla, CA, USA. [e-mail].
Howard Hughes Medical Institute, University of California San Diego, La Jolla, CA, USA. [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C4  (Explore in 3D)
Global Stoichiometry: Hetero 12-mer - A4B4C4 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 12-mer - A4B4C1D1E1F1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 837.41 kDa 
• Atom Count: 17,272 
• Modeled Residue Count: 2,216 
• Deposited Residue Count: 7,608 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Chimallin	A, B, C, D, E, F, G, H, I, J, K, L	634	Pseudomonas phage 201phi2-1	Mutation(s): 0  Gene Names: 201phi2-1p105
UniProt
Find proteins for B3FIW8 (Pseudomonas phage 201phi2-1) Explore B3FIW8  Go to UniProtKB:  B3FIW8

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.40 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	RELION
MODEL REFINEMENT	PHENIX

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-07-27 
Deposition Author(s): 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.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01GM129245
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	R21AI148814
National Science Foundation (NSF, United States)	United States	NSF DBI 1920374
Howard Hughes Medical Institute (HHMI)	United States	--

Revision History  

• Version 1.0: 2022-07-27
  Type: Initial release
  
• Version 1.1: 2022-08-17
  Changes: Database references
• Version 1.2: 2022-08-24
  Changes: Database references
• Version 1.3: 2024-06-05
  Changes: Data collection