4BTG | pdb_00004btg

Coordinates of the bacteriophage phi6 capsid subunits (P1A and P1B) fitted into the cryoEM reconstruction of the procapsid at 4.4 A resolution

• PDB DOI: https://doi.org/10.2210/pdb4BTG/pdb
• EM Map EMD-2364: EMDB EMDataResource

• Classification: VIRUS
• Organism(s): Cystovirus phi6
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2013-06-17 Released: 2013-08-14 
• Deposition Author(s): Nemecek, D., Boura, E., Wu, W., Cheng, N., Plevka, P., Qiao, J., Mindich, L., Heymann, J.B., Hurley, J.H., Steven, A.C.

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 4.40 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental

Literature

Subunit Folds and Maturation Pathway of a Dsrna Virus Capsid.

Nemecek, D., Boura, E., Wu, W., Cheng, N., Plevka, P., Qiao, J., Mindich, L., Heymann, J.B., Hurley, J.H., Steven, A.C.

(2013) Structure 21: 1374

• PubMed: 23891288 
• DOI: https://doi.org/10.1016/j.str.2013.06.007
• Primary Citation Related Structures: 
  4BTG, 4BTQ, 4K7H


• PubMed Abstract: 
  

  The cystovirus ϕ6 shares several distinct features with other double-stranded RNA (dsRNA) viruses, including the human pathogen, rotavirus: segmented genomes, nonequivalent packing of 120 subunits in its icosahedral capsid, and capsids as compartments for transcription and replication. ϕ6 assembles as a dodecahedral procapsid that undergoes major conformational changes as it matures into the spherical capsid. We determined the crystal structure of the capsid protein, P1, revealing a flattened trapezoid subunit with an α-helical fold. We also solved the procapsid with cryo-electron microscopy to comparable resolution. Fitting the crystal structure into the procapsid disclosed substantial conformational differences between the two P1 conformers. Maturation via two intermediate states involves remodeling on a similar scale, besides huge rigid-body rotations. The capsid structure and its stepwise maturation that is coupled to sequential packaging of three RNA segments sets the cystoviruses apart from other dsRNA viruses as a dynamic molecular machine.

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Organizational Affiliation: 
• National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, 50 South Drive, Bethesda, MD 20892, USA.

Biological Assembly 1  

Global Symmetry: Icosahedral - I  (Explore in 3D)
Global Stoichiometry: Homo 120-mer - A120 

Biological assembly 1 assigned by authors and generated by (software)

Macromolecule Content 

• Total Structure Weight: 168.33 kDa 
• Atom Count: 11,840 
• Modeled Residue Count: 1,522 
• Deposited Residue Count: 1,522 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MAJOR INNER PROTEIN P1	A, B	761	Cystovirus phi6	Mutation(s): 0
UniProt
Find proteins for P11126 (Pseudomonas phage phi6) Explore P11126  Go to UniProtKB:  P11126

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 4.40 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	Bsoft
RECONSTRUCTION	EMAN

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-08-14 
Deposition Author(s): Nemecek, D., Boura, E., Wu, W., Cheng, N., Plevka, P., Qiao, J., Mindich, L., Heymann, J.B., Hurley, J.H., Steven, A.C.

Revision History  

• Version 1.0: 2013-08-14
  Type: Initial release
  
• Version 1.1: 2013-08-28
  Changes: Database references
• Version 1.2: 2017-08-23
  Changes: Data collection
• Version 1.3: 2024-05-08
  Changes: Data collection, Database references, Derived calculations, Refinement description