6E8K

Legionella Longbeachae LeSH (Llo2327) bound to the human interleukin-2 receptor beta pTyr387 peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.71 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.189 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Identification and characterization of a large family of superbinding bacterial SH2 domains.

Kaneko, T.Stogios, P.J.Ruan, X.Voss, C.Evdokimova, E.Skarina, T.Chung, A.Liu, X.Li, L.Savchenko, A.Ensminger, A.W.Li, S.S.

(2018) Nat Commun 9: 4549-4549

  • DOI: 10.1038/s41467-018-06943-2
  • Primary Citation of Related Structures:  
    6E8H, 6E8I, 6E8K, 6E8M

  • PubMed Abstract: 
  • Src homology 2 (SH2) domains play a critical role in signal transduction in mammalian cells by binding to phosphorylated Tyr (pTyr). Apart from a few isolated cases in viruses, no functional SH2 domain has been identified to date in prokaryotes. Here ...

    Src homology 2 (SH2) domains play a critical role in signal transduction in mammalian cells by binding to phosphorylated Tyr (pTyr). Apart from a few isolated cases in viruses, no functional SH2 domain has been identified to date in prokaryotes. Here we identify 93 SH2 domains from Legionella that are distinct in sequence and specificity from mammalian SH2 domains. The bacterial SH2 domains are not only capable of binding proteins or peptides in a Tyr phosphorylation-dependent manner, some bind pTyr itself with micromolar affinities, a property not observed for mammalian SH2 domains. The Legionella SH2 domains feature the SH2 fold and a pTyr-binding pocket, but lack a specificity pocket found in a typical mammalian SH2 domain for recognition of sequences flanking the pTyr residue. Our work expands the boundary of phosphotyrosine signalling to prokaryotes, suggesting that some bacterial effector proteins have acquired pTyr-superbinding characteristics to facilitate bacterium-host interactions.


    Organizational Affiliation

    Children's Health Research Institute, Lawson Health Research Institute, 800 Commissioner's Road East, London, ON, N6C 2V5, Canada. sli@uwo.ca.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
LeSH (Llo2327)A169Legionella longbeachae NSW150Mutation(s): 0 
Gene Names: LLO_2327
Find proteins for D3HJY4 (Legionella longbeachae serogroup 1 (strain NSW150))
Explore D3HJY4 
Go to UniProtKB:  D3HJY4
Protein Feature View
Expand
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
interleukin-2 receptor beta pTyr387 peptideB13Homo sapiensMutation(s): 0 
Gene Names: IL2RBIL15RB
Find proteins for P14784 (Homo sapiens)
Explore P14784 
Go to UniProtKB:  P14784
NIH Common Fund Data Resources
PHAROS  P14784
Protein Feature View
Expand
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
PTR
Query on PTR
BL-PEPTIDE LINKINGC9 H12 N O6 PTYR
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.71 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.189 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 40.45α = 90
b = 64.24β = 90
c = 67.53γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
MOSFLMdata reduction
SCALAdata scaling
Auto-Rickshawphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2018-07-30 
  • Released Date: 2018-11-14 
  • Deposition Author(s): Kaneko, T., Li, S.S.C.

Revision History 

  • Version 1.0: 2018-11-14
    Type: Initial release
  • Version 1.1: 2019-12-04
    Changes: Author supporting evidence