8FXR

Structure of neck with portal vertex of capsid of Agrobacterium phage Milano


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 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 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
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Linking protein 2, gp12838Agrobacterium phage MilanoMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Neck 1 protein, gp14202Agrobacterium phage MilanoMutation(s): 0 
UniProt
Find proteins for A0A482MHL8 (Agrobacterium phage Milano)
Explore A0A482MHL8 
Go to UniProtKB:  A0A482MHL8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A482MHL8
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Neck 2 protein, gp15141Agrobacterium phage MilanoMutation(s): 0 
UniProt
Find proteins for A0A482MFQ3 (Agrobacterium phage Milano)
Explore A0A482MFQ3 
Go to UniProtKB:  A0A482MFQ3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A482MFQ3
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Linking protein 1, gp16DF [auth f7],
KE [auth f6],
QA [auth f2],
RD [auth f5],
X [auth f1]
217Agrobacterium phage MilanoMutation(s): 0 
UniProt
Find proteins for A0A482MFR0 (Agrobacterium phage Milano)
Explore A0A482MFR0 
Go to UniProtKB:  A0A482MFR0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A482MFR0
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Major capsid protein, gp9465Agrobacterium phage MilanoMutation(s): 0 
UniProt
Find proteins for A0A482MFS6 (Agrobacterium phage Milano)
Explore A0A482MFS6 
Go to UniProtKB:  A0A482MFS6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A482MFS6
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Minor capsid protein, gp10137Agrobacterium phage MilanoMutation(s): 0 
UniProt
Find proteins for A0A482MFS0 (Agrobacterium phage Milano)
Explore A0A482MFS0 
Go to UniProtKB:  A0A482MFS0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A482MFS0
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Collar sheath protein, gp13230Agrobacterium phage MilanoMutation(s): 0 
UniProt
Find proteins for A0A482MGH3 (Agrobacterium phage Milano)
Explore A0A482MGH3 
Go to UniProtKB:  A0A482MGH3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A482MGH3
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Portal protein, gp7420Agrobacterium phage MilanoMutation(s): 0 
UniProt
Find proteins for A0A482MFW7 (Agrobacterium phage Milano)
Explore A0A482MFW7 
Go to UniProtKB:  A0A482MFW7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A482MFW7
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Tail-terminator protein, gp18178Agrobacterium phage MilanoMutation(s): 0 
UniProt
Find proteins for A0A482MF73 (Agrobacterium phage Milano)
Explore A0A482MF73 
Go to UniProtKB:  A0A482MF73
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A482MF73
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Tail-tube, gp21136Agrobacterium phage MilanoMutation(s): 0 
UniProt
Find proteins for A0A482MHE7 (Agrobacterium phage Milano)
Explore A0A482MHE7 
Go to UniProtKB:  A0A482MHE7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A482MHE7
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



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