4NSO

Crystal structure of the effector-immunity protein complex

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.220 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history. 


Literature

Structural basis for recognition of the type VI spike protein VgrG3 by a cognate immunity protein.

Zhang, J., Zhang, H., Gao, Z., Hu, H., Dong, C., Dong, Y.H.

(2014) FEBS Lett 588: 1891-1898

  • DOI: 10.1016/j.febslet.2014.04.016
  • Primary Citation of Related Structures:  
    4NSO, 4NSR

  • PubMed Abstract: 

    • The bacterial type VI secretion system (T6SS) is used by donor cells to inject toxic effectors into receptor cells. The donor cells produce the corresponding immunity proteins to protect themselves against the effector proteins, thereby preventing their self-intoxication ...

    The bacterial type VI secretion system (T6SS) is used by donor cells to inject toxic effectors into receptor cells. The donor cells produce the corresponding immunity proteins to protect themselves against the effector proteins, thereby preventing their self-intoxication. Recently, the C-terminal domain of VgrG3 was identified as a T6SS effector. Information on the molecular mechanism of VgrG3 and its immunity protein TsaB has been lacking. Here, we determined the crystal structures of native TsaB and the VgrG3C-TsaB complex. VgrG3C adopts a canonical phage-T4-lysozyme-like fold. TsaB interacts with VgrG3C through molecular mimicry, and inserts into the VgrG3C pocket.

    Organizational Affiliation: 

    Beijing Synchrotron Radiation Facility, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing 100049, People's Republic of China. Electronic address: dongyh@ihep.ac.cn.



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Effector proteinA301Vibrio cholerae O1 biovar El Tor str. N16961Mutation(s): 0 
Gene Names: VCPCS023_003519, VC_A0123, vgrG3
EC: 3.2.1
UniProt
Find proteins for Q9KN42 (Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961))
Explore Q9KN42 
Go to UniProtKB:  Q9KN42
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9KN42
Protein Feature View
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  • Reference Sequence
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(by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Immunity proteinB108Vibrio cholerae O1 biovar El Tor str. N16961Mutation(s): 0 
Gene Names: VC_A0124, tsiV3
UniProt
Find proteins for Q9KN41 (Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961))
Explore Q9KN41 
Go to UniProtKB:  Q9KN41
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9KN41
Protein Feature View
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  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE		A L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.220 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 133.631α = 90
b = 78.66β = 101.52
c = 47.86γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
PHENIXmodel building
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

  • Deposited Date: 2013-11-28 
  • Released Date: 2014-04-16 
    • Deposition Author(s): Dong, C.

Revision History  (Full details and data files)

  • Version 1.0: 2014-04-16
    Type: Initial release
  • Version 1.1: 2014-05-21
    Changes: Database references
  • Version 1.2: 2014-06-11
    Changes: Database references