6IJF

Crystal structure of the type VI effector-immunity complex (Tae4-Tai4) from Agrobacterium tumefaciens


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.191 

wwPDB Validation 3D Report Full Report



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: 10.1107/S2053230X18016369
  • Structures With Same Primary Citation

  • 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 cyto ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Tai4A, B107Agrobacterium tumefaciensMutation(s): 0 
Gene Names: SY94_4314
Find proteins for A0A083ZID3 (Rhizobium radiobacter)
Explore A0A083ZID3 
Go to UniProtKB:  A0A083ZID3
Protein Feature View
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  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Tae4C, D164Agrobacterium tumefaciensMutation(s): 0 
Gene Names: SY94_4315
Find proteins for A0A083ZID4 (Rhizobium radiobacter)
Explore A0A083ZID4 
Go to UniProtKB:  A0A083ZID4
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
1PE
Query on 1PE

Download CCD File 
A
PENTAETHYLENE GLYCOL
C10 H22 O6
JLFNLZLINWHATN-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download CCD File 
C
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.191 
  • Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.025α = 90
b = 72.025β = 90
c = 194.348γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
DIALSdata reduction
MOLREPphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-12-19
    Type: Initial release