8FWG

Structure of neck and portal vertex of Agrobacterium phage Milano, C5 symmetry


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.45 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


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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 of 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.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Linking protein 2, gp12838Agrobacterium phage MilanoMutation(s): 0 
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Linking protein 1, gp16DD [auth f5],
E [auth f1],
PE [auth f7],
WD [auth f6],
X [auth f2]
217Agrobacterium phage MilanoMutation(s): 0 
UniProt
Find proteins for A0A482MFR0 (Agrobacterium phage Milano)
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Go to UniProtKB:  A0A482MFR0
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UniProt GroupA0A482MFR0
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Major capsid protein, gp9465Agrobacterium phage MilanoMutation(s): 0 
UniProt
Find proteins for A0A482MFS6 (Agrobacterium phage Milano)
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UniProt GroupA0A482MFS6
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Minor capsid protein, gp10137Agrobacterium phage MilanoMutation(s): 0 
UniProt
Find proteins for A0A482MFS0 (Agrobacterium phage Milano)
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UniProt GroupA0A482MFS0
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Collar sheath protein, gp13230Agrobacterium phage MilanoMutation(s): 0 
UniProt
Find proteins for A0A482MGH3 (Agrobacterium phage Milano)
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UniProt GroupA0A482MGH3
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Neck 1 protein, gp14UC [auth A4],
VC [auth B4],
WC [auth C4],
XC [auth D4],
YC [auth E4]
202Agrobacterium phage MilanoMutation(s): 0 
UniProt
Find proteins for A0A482MHL8 (Agrobacterium phage Milano)
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UniProt GroupA0A482MHL8
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.45 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