3JA7 | pdb_00003ja7

Cryo-EM structure of the bacteriophage T4 portal protein assembly at near-atomic resolution

• PDB DOI: https://doi.org/10.2210/pdb3JA7/pdb
• EM Map EMD-6324: EMDB EMDataResource

• Classification: VIRAL PROTEIN
• Organism(s): Tequatrovirus T4
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2015-04-21 Released: 2015-07-22 
• Deposition Author(s): Sun, L., Zhang, X., Gao, S., Rao, P.A., Padilla-Sanchez, V., Chen, Z., Sun, S., Xiang, Y., Subramaniam, S., Rao, V.B., Rossmann, M.G.

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.60 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Cryo-EM structure of the bacteriophage T4 portal protein assembly at near-atomic resolution.

Sun, L., Zhang, X., Gao, S., Rao, P.A., Padilla-Sanchez, V., Chen, Z., Sun, S., Xiang, Y., Subramaniam, S., Rao, V.B., Rossmann, M.G.

(2015) Nat Commun 6: 7548-7548

• PubMed: 26144253 
• DOI: https://doi.org/10.1038/ncomms8548
• Primary Citation Related Structures: 
  3JA7


• PubMed Abstract: 
  

  The structure and assembly of bacteriophage T4 has been extensively studied. However, the detailed structure of the portal protein remained unknown. Here we report the structure of the bacteriophage T4 portal assembly, gene product 20 (gp20), determined by cryo-electron microscopy (cryo-EM) to 3.6 Å resolution. In addition, analysis of a 10 Å resolution cryo-EM map of an empty prolate T4 head shows how the dodecameric portal assembly interacts with the capsid protein gp23 at the special pentameric vertex. The gp20 structure also verifies that the portal assembly is required for initiating head assembly, for attachment of the packaging motor, and for participation in DNA packaging. Comparison of the Myoviridae T4 portal structure with the known portal structures of φ29, SPP1 and P22, representing Podo- and Siphoviridae, shows that the portal structure probably dates back to a time when self-replicating microorganisms were being established on Earth.

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Organizational Affiliation: 
• Department of Biological Sciences, Purdue University, 240S. Martin Jischke Drive, West Lafayette, Indiana 47907-2032, USA.
Department of Biology, The Catholic University of America, 620 Michigan Ave. N.E., Washington, DC 20064, USA.
National Cancer Institute, National Institutes of Health, 50 South Drive, Bldg. 50 Room 4306, Bethesda, Maryland 20892, USA.

Biological Assembly 1  

Global Symmetry: Cyclic - C12  (Explore in 3D)
Global Stoichiometry: Homo 12-mer - A12 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 640.3 kDa 
• Atom Count: 41,280 
• Modeled Residue Count: 5,136 
• Deposited Residue Count: 5,460 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Portal protein gp20	A, B, C, D, E, F, G, H, I, J, K, L	455	Tequatrovirus T4	Mutation(s): 0  Gene Names: 20
UniProt
Find proteins for P13334 (Enterobacteria phage T4) Explore P13334  Go to UniProtKB:  P13334

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.60 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	RELION

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-07-22 
Deposition Author(s): Sun, L., Zhang, X., Gao, S., Rao, P.A., Padilla-Sanchez, V., Chen, Z., Sun, S., Xiang, Y., Subramaniam, S., Rao, V.B., Rossmann, M.G.

Revision History  

• Version 1.0: 2015-07-22
  Type: Initial release
  
• Version 1.1: 2018-07-18
  Changes: Data collection
• Version 1.2: 2019-12-18
  Changes: Database references, Other
• Version 1.3: 2024-02-21
  Changes: Data collection, Database references, Refinement description