6F45

Crystal structure of the gp37-gp38 adhesin tip complex of the bacteriophage S16 long tail fiber


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.185 
  • R-Value Work: 0.152 
  • R-Value Observed: 0.153 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Salmonella Phage S16 Tail Fiber Adhesin Features a Rare Polyglycine Rich Domain for Host Recognition.

Dunne, M.Denyes, J.M.Arndt, H.Loessner, M.J.Leiman, P.G.Klumpp, J.

(2018) Structure 26: 1573-1582.e4

  • DOI: https://doi.org/10.1016/j.str.2018.07.017
  • Primary Citation of Related Structures:  
    6F45

  • PubMed Abstract: 

    The ability of phages to infect specific bacteria has led to their exploitation as bio-tools for bacterial remediation and detection. Many phages recognize bacterial hosts via adhesin tips of their long tail fibers (LTFs). Adhesin sequence plasticity modulates receptor specificity, and thus primarily defines a phage's host range. Here we present the crystal structure of an adhesin (gp38) attached to a trimeric β-helical tip (gp37) from the Salmonella phage S16 LTF. Gp38 contains rare polyglycine type II helices folded into a packed lattice, herein designated "PG II sandwich." Sequence variability within the domain is limited to surface-exposed helices and distal loops that form putative receptor-binding sites. In silico analyses revealed a prevalence of the adhesin architecture among T-even phages, excluding the archetypal T4 phage. Overall, S16 LTF provides a valuable model for understanding binding mechanisms of phage adhesins, and for engineering of phage adhesins with expandable or modulated host ranges.


  • Organizational Affiliation

    Institute of Food, Nutrition and Health, ETH Zurich, Zurich, Switzerland. Electronic address: matthew.dunne@hest.ethz.ch.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Receptor recognition proteinA [auth D]249Salmonella phage vB_SenM-S16Mutation(s): 0 
UniProt
Find proteins for M1EBB2 (Salmonella phage S16)
Explore M1EBB2 
Go to UniProtKB:  M1EBB2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupM1EBB2
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Long tail fiber distal subunitB [auth A],
C [auth B],
D [auth C]
204Salmonella phage vB_SenM-S16Mutation(s): 0 
UniProt
Find proteins for M1EAS5 (Salmonella phage S16)
Explore M1EAS5 
Go to UniProtKB:  M1EAS5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupM1EAS5
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MPD
Query on MPD

Download Ideal Coordinates CCD File 
I [auth D],
P [auth A],
Q [auth A],
T [auth B],
W [auth C]
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
MRD
Query on MRD

Download Ideal Coordinates CCD File 
F [auth D],
G [auth D],
H [auth D],
O [auth A],
V [auth C]
(4R)-2-METHYLPENTANE-2,4-DIOL
C6 H14 O2
SVTBMSDMJJWYQN-RXMQYKEDSA-N
IMD
Query on IMD

Download Ideal Coordinates CCD File 
J [auth D],
K [auth D],
R [auth A]
IMIDAZOLE
C3 H5 N2
RAXXELZNTBOGNW-UHFFFAOYSA-O
MG
Query on MG

Download Ideal Coordinates CCD File 
E [auth D]
L [auth A]
M [auth A]
N [auth A]
S [auth B]
E [auth D],
L [auth A],
M [auth A],
N [auth A],
S [auth B],
U [auth C]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.185 
  • R-Value Work: 0.152 
  • R-Value Observed: 0.153 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 81.337α = 90
b = 98.904β = 90
c = 140.036γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
SCALAdata scaling
PARROTphasing
ARP/wARPmodel building
Cootmodel building

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
ETH ZurichSwitzerlandETH-08 14-1

Revision History  (Full details and data files)

  • Version 1.0: 2018-08-01
    Type: Initial release
  • Version 1.1: 2018-10-03
    Changes: Data collection, Database references
  • Version 1.2: 2018-12-19
    Changes: Data collection, Database references
  • Version 1.3: 2024-05-08
    Changes: Data collection, Database references, Derived calculations