6OMA

non-decorated head of the phage T5

• PDB DOI: https://doi.org/10.2210/pdb6OMA/pdb
• EM Map EMD-20122: EMDB EMDataResource

• Classification: VIRUS
• Organism(s): Tequintavirus T5
• Mutation(s): No 


• Deposited: 2019-04-18 Released: 2019-10-02 
• Deposition Author(s): Huet, A., Duda, R.L., Boulanger, P., Conway, J.F.
• Funding Organization(s): National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 7.20 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Capsid expansion of bacteriophage T5 revealed by high resolution cryoelectron microscopy.

Huet, A., Duda, R.L., Boulanger, P., Conway, J.F.

(2019) Proc Natl Acad Sci U S A 116: 21037-21046

• PubMed: 31578255 
• DOI: https://doi.org/10.1073/pnas.1909645116
• Primary Citation of Related Structures:  
  6OKB, 6OMA, 6OMC


• PubMed Abstract: 
  

  The large (90-nm) icosahedral capsid of bacteriophage T5 is composed of 775 copies of the major capsid protein (mcp) together with portal, protease, and decoration proteins. Its assembly is a regulated process that involves several intermediates, including a thick-walled round precursor prohead that expands as the viral DNA is packaged to yield a thin-walled and angular mature capsid. We investigated capsid maturation by comparing cryoelectron microscopy (cryo-EM) structures of the prohead, the empty expanded capsid both with and without decoration protein, and the virion capsid at a resolution of 3.8 Å for the latter. We detail the molecular structure of the mcp, its complex pattern of interactions, and their evolution during maturation. The bacteriophage T5 mcp is a variant of the canonical HK97-fold with a high level of plasticity that allows for the precise assembly of a giant macromolecule and the adaptability needed to interact with other proteins and the packaged DNA.

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Organizational Affiliation: 

Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260.

Biological Assembly 1  

Global Symmetry: Icosahedral - I  (Explore in 3D)
Global Stoichiometry: Homo 780-mer - A780 

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

Biological Assembly Evidence: microscopy

Macromolecule Content

• Total Structure Weight: 428.11 kDa 
• Atom Count: 30,092 
• Modelled Residue Count: 3,883 
• Deposited Residue Count: 3,887 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Major capsid protein	A, B, C, D, E, F, G, H, I, J, K, L, M	299	Tequintavirus T5	Mutation(s): 0
UniProt
Find proteins for Q6QGD8 (Escherichia phage T5) Explore Q6QGD8  Go to UniProtKB:  Q6QGD8

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 7.20 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	Auto3DEM
MODEL REFINEMENT	UCSF Chimera
MODEL REFINEMENT	MDFF
MODEL REFINEMENT	PHENIX

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-10-02 
Deposition Author(s): Huet, A., Duda, R.L., Boulanger, P., Conway, J.F.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)	United States	R01 GM047795
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)	United States	S10 OD019995

Revision History  

• Version 1.0: 2019-10-02
  Type: Initial release
  
• Version 1.1: 2019-11-13
  Changes: Database references
• Version 1.2: 2019-12-18
  Changes: Author supporting evidence
• Version 1.3: 2024-03-20
  Changes: Data collection, Database references, Derived calculations, Refinement description