6IJE | pdb_00006ije

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

• PDB DOI: https://doi.org/10.2210/pdb6IJE/pdb

• Classification: ANTITOXIN
• Organism(s): Agrobacterium tumefaciens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2018-10-09 Released: 2018-12-19 
• Deposition Author(s): Fukuhara, S., Nakane, T., Yamashita, K., Ishii, R., Ishitani, R., Nureki, O.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free: 
  0.198 (Depositor), 0.206 (DCC) 
• R-Value Work: 
  0.174 (Depositor), 0.186 (DCC) 
• R-Value Observed: 
  0.175 (Depositor) 

Starting Model: experimental

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

• PubMed: 30511676 
• DOI: https://doi.org/10.1107/S2053230X18016369
• Primary Citation 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.

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

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 23.82 kDa 
• Atom Count: 1,715 
• Modeled Residue Count: 200 
• Deposited Residue Count: 218 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tai4	A [auth B], B [auth A]	109	Agrobacterium tumefaciens	Mutation(s): 0  Gene Names: SY94_4314

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	C [auth B], D [auth B], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free:  0.198 (Depositor), 0.206 (DCC) 
• R-Value Work:  0.174 (Depositor), 0.186 (DCC) 
• R-Value Observed: 0.175 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.921	α = 90
b = 57.756	β = 90
c = 71.465	γ = 90

Software Package:

Software Name	Purpose
Aimless	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
DIALS	data reduction
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-12-19 
Deposition Author(s): Fukuhara, S., Nakane, T., Yamashita, K., Ishii, R., Ishitani, R., Nureki, O.

Revision History  

• Version 1.0: 2018-12-19
  Type: Initial release
  
• Version 1.1: 2023-11-22
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2024-11-20
  Changes: Structure summary