6IJE

Crystal structure of the type VI amidase immunity (Tai4) from Agrobacterium tumefaciens


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.175 

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This is version 1.1 of the entry. See complete history


Literature

Crystal structure of the Agrobacterium tumefaciens type VI effector-immunity complex.

Fukuhara, S.Nakane, T.Yamashita, K.Ishii, R.Ishitani, R.Nureki, O.

(2018) Acta Crystallogr F Struct Biol Commun 74: 810-816

  • DOI: https://doi.org/10.1107/S2053230X18016369
  • Primary Citation of Related Structures:  
    6IJE, 6IJF

  • PubMed Abstract: 

    The type VI secretion system (T6SS) comprises needle-shaped multisubunit complexes that play a role in the microbial defense systems of Gram-negative bacteria. Some Gram-negative bacteria harboring a T6SS deliver toxic effector proteins into the cytoplasm or periplasm of competing bacteria in order to lyse and kill them. To avoid self-cell disruption, these bacteria have cognate immunity proteins that inhibit their toxic effector proteins. T6SS amidase effector protein 4 (Tae4) and T6SS amidase immunity protein 4 (Tai4) are a representative of the toxic effector-immunity pairs of the T6SS. Here, the three-dimensional structures of Tai4 and the Tae4-Tai4 complex from Agrobacterium tumefaciens are reported at 1.55 and 1.9 Å resolution, respectively. A structural comparison with other Tae4-Tai4 homologs revealed similarities and differences in the catalytic and inhibitory mechanisms among the Tae4 and Tai4 family proteins.


  • Organizational Affiliation

    Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Tai4A [auth B],
B [auth A]
109Agrobacterium tumefaciensMutation(s): 0 
Gene Names: SY94_4314
UniProt
Find proteins for A0A083ZID3 (Rhizobium radiobacter)
Explore A0A083ZID3 
Go to UniProtKB:  A0A083ZID3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A083ZID3
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.175 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 53.921α = 90
b = 57.756β = 90
c = 71.465γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
DIALSdata reduction
MOLREPphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-12-19
    Type: Initial release
  • Version 1.1: 2023-11-22
    Changes: Data collection, Database references, Refinement description