8FXP | pdb_00008fxp

Structure of capsid of Agrobacterium phage Milano


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.04 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

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This is version 1.1 of the entry. See complete history

Literature

Neck and capsid architecture of the robust Agrobacterium phage Milano.

Sonani, R.R.Esteves, N.C.Horton, A.A.Kelly, R.J.Sebastian, A.L.Wang, F.Kreutzberger, M.A.B.Leiman, P.G.Scharf, B.E.Egelman, E.H.

(2023) Commun Biol 6: 921-921

  • DOI: https://doi.org/10.1038/s42003-023-05292-1
  • Primary Citation Related Structures: 
    8FWB, 8FWC, 8FWE, 8FWG, 8FWM, 8FXP, 8FXR

  • PubMed Abstract: 

    Large gaps exist in our understanding of how bacteriophages, the most abundant biological entities on Earth, assemble and function. The structure of the "neck" region, where the DNA-filled capsid is connected to the host-recognizing tail remains poorly understood. We describe cryo-EM structures of the neck, the neck-capsid and neck-tail junctions, and capsid of the Agrobacterium phage Milano. The Milano neck 1 protein connects the 12-fold symmetrical neck to a 5-fold vertex of the icosahedral capsid. Comparison of Milano neck 1 homologs leads to four proposed classes, likely evolved from the simplest one in siphophages to more complex ones in myo- and podophages. Milano neck is surrounded by the atypical collar, which covalently crosslinks the tail sheath to neck 1. The Milano capsid is decorated with three types of proteins, a minor capsid protein (mCP) and two linking proteins crosslinking the mCP to the major capsid protein. The extensive network of disulfide bonds within and between neck, collar, capsid and tail provides an exceptional structural stability to Milano.


  • Organizational Affiliation
    • Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA, 22903, USA.

Macromolecule Content 

  • Total Structure Weight: 1,501.94 kDa 
  • Atom Count: 72,532 
  • Modeled Residue Count: 9,474 
  • Deposited Residue Count: 13,735 
  • Unique protein chains: 4

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Linking protein 1, gp16217Agrobacterium phage MilanoMutation(s): 0 
Find similar proteins by:|  3D Structure
Find similar proteins by:|  3D Structure
Find similar proteins by:|  3D Structure

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.04 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM122510

Revision History  (Full details and data files)

  • Version 1.0: 2023-12-06
    Type: Initial release
  • Version 1.1: 2024-11-20
    Changes: Data collection, Structure summary