8B14

T5 Receptor Binding Protein pb5 in complex with its E. coli receptor FhuA


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Deciphering Bacteriophage T5 Host Recognition Mechanism and Infection Trigger.

Degroux, S.Effantin, G.Linares, R.Schoehn, G.Breyton, C.

(2023) J Virol 97: e0158422-e0158422

  • DOI: https://doi.org/10.1128/jvi.01584-22
  • Primary Citation of Related Structures:  
    8B14

  • PubMed Abstract: 

    Bacteriophages, viruses infecting bacteria, recognize their host with high specificity, binding to either saccharide motifs or proteins of the cell wall of their host. In the majority of bacteriophages, this host recognition is performed by receptor binding proteins (RBPs) located at the extremity of a tail. Interaction between the RBPs and the host is the trigger for bacteriophage infection, but the molecular details of the mechanisms are unknown for most bacteriophages. Here, we present the electron cryomicroscopy (cryo-EM) structure of bacteriophage T5 RBP pb5 in complex with its Escherichia coli receptor, the iron ferrichrome transporter FhuA. Monomeric RBP pb5 is located at the extremity of T5's long flexible tail, and its irreversible binding to FhuA commits T5 to infection. Analysis of the structure of RBP pb5 within the complex, comparison with its AlphaFold2-predicted structure, and its fit into a previously determined map of the T5 tail tip in complex with FhuA allow us to propose a mechanism of transmission of the RBP pb5 receptor binding to the straight fiber, initiating the cascade of events that commits T5 to DNA ejection. IMPORTANCE Tailed bacteriophages specifically recognize their bacterial host by interaction of their receptor binding protein(s) (RBPs) with saccharides and/or proteins located at the surface of their prey. This crucial interaction commits the virus to infection, but the molecular details of this mechanism are unknown for the majority of bacteriophages. We determined the structure of bacteriophage T5 RBP pb5 in complex with its E. coli receptor, FhuA, by cryo-EM. This first structure of an RBP bound to its protein receptor allowed us to propose a mechanism of transmission of host recognition to the rest of the phage, ultimately opening the capsid and perforating the cell wall and, thus, allowing safe channeling of the DNA into the host cytoplasm.


  • Organizational Affiliation

    Université Grenoble Alpes, CNRS, CEA, IBS, Grenoble, France.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
FhuA iron-ferrichrome transporter723Escherichia coliMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P06971 (Escherichia coli (strain K12))
Explore P06971 
Go to UniProtKB:  P06971
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP06971
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
pb5 bacteriophage T5 receptor binding protein640Escherichia phage T5Mutation(s): 0 
UniProt
Find proteins for P23207 (Escherichia phage T5)
Explore P23207 
Go to UniProtKB:  P23207
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP23207
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
LU9
Query on LU9

Download Ideal Coordinates CCD File 
D [auth A][(2R,3S,4R,5R,6R)-2-[[(2R,4R,5R,6R)-6-[(1R)-1,2-bis(oxidanyl)ethyl]-4-[(2R,4R,5R,6R)-6-[(1R)-1,2-bis(oxidanyl)ethyl]-2-carboxy-4,5-bis(oxidanyl)oxan-2-yl]oxy-2-carboxy-5-oxidanyl-oxan-2-yl]oxymethyl]-5-[[(3R)-3-dodecanoyloxytetradecanoyl]amino]-4-(3-nonanoyloxypropanoyloxy)-6-[[(2R,3S,4R,5R,6R)-3-oxidanyl-4-[(3S)-3-oxidanyltetradecanoyl]oxy-5-[[(3R)-3-oxidanyltridecanoyl]amino]-6-phosphonatooxy-oxan-2-yl]methoxy]oxan-3-yl] phosphate
C93 H164 N2 O39 P2
VKIJVPHKEVBYMR-HZMIYFLPSA-J
DDQ (Subject of Investigation/LOI)
Query on DDQ

Download Ideal Coordinates CCD File 
C [auth A]DECYLAMINE-N,N-DIMETHYL-N-OXIDE
C12 H27 N O
ZRKZFNZPJKEWPC-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTCoot0.9.2
MODEL REFINEMENTPHENIX1.18.2-3874
RECONSTRUCTIONRELION3

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Agence Nationale de la Recherche (ANR)FranceANR-16-CE11-0027
Agence Nationale de la Recherche (ANR)FranceANR-21-CE11-0023

Revision History  (Full details and data files)

  • Version 1.0: 2023-02-08
    Type: Initial release
  • Version 1.1: 2024-02-21
    Changes: Data collection, Database references, Refinement description