6ZN8 | pdb_00006zn8

Crystal structure of the H. influenzae VapXD toxin-antitoxin complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.21 Å
  • R-Value Free: 
    0.299 (Depositor), 0.309 (DCC) 
  • R-Value Work: 
    0.258 (Depositor), 0.267 (DCC) 
  • R-Value Observed: 
    0.262 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 6ZN8

This is version 1.4 of the entry. See complete history

Literature

Structural Basis for Toxin Inhibition in the VapXD Toxin-Antitoxin System.

Bertelsen, M.B.Senissar, M.Nielsen, M.H.Bisiak, F.Cunha, M.V.Molinaro, A.L.Daines, D.A.Brodersen, D.E.

(2021) Structure 29: 139

  • DOI: https://doi.org/10.1016/j.str.2020.10.002
  • Primary Citation Related Structures: 
    6ZI0, 6ZI1, 6ZN8

  • PubMed Abstract: 

    Bacterial type II toxin-antitoxin (TA) modules encode a toxic protein that downregulates metabolism and a specific antitoxin that binds and inhibits the toxin during normal growth. In non-typeable Haemophilus influenzae, a common cause of infections in humans, the vapXD locus was found to constitute a functional TA module and contribute to pathogenicity; however, the mode of action of VapD and the mechanism of inhibition by the VapX antitoxin remain unknown. Here, we report the structure of the intact H. influenzae VapXD complex, revealing an unusual 2:1 TA molecular stoichiometry where a Cas2-like homodimer of VapD binds a single VapX antitoxin. VapX consists of an oligonucleotide/oligosaccharide-binding domain that docks into an asymmetrical cavity on the toxin dimer. Structures of isolated VapD further reveal how a symmetrical toxin homodimer adapts to interacting with an asymmetrical antitoxin and suggest how a primordial TA system evolved to become part of CRISPR-Cas immunity systems.


  • Organizational Affiliation
    • Department of Molecular Biology and Genetics, Aarhus University, DK-8000 Aarhus C, Denmark.

Macromolecule Content 

  • Total Structure Weight: 65.84 kDa 
  • Atom Count: 3,939 
  • Modeled Residue Count: 489 
  • Deposited Residue Count: 562 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Endoribonuclease VapDA,
B,
C [auth D],
D [auth E]
100Haemophilus influenzae 86-028NPMutation(s): 0 
Gene Names: vapDNTHI0577
EC: 3.1
UniProt
Find proteins for Q4QN95 (Haemophilus influenzae (strain 86-028NP))
Explore Q4QN95 
Go to UniProtKB:  Q4QN95
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ4QN95
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
VapXE [auth C],
F
81Haemophilus influenzae 86-028NPMutation(s): 0 
Gene Names: vapXNTHI0578
UniProt
Find proteins for Q4QN94 (Haemophilus influenzae (strain 86-028NP))
Explore Q4QN94 
Go to UniProtKB:  Q4QN94
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ4QN94
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A,
B,
C [auth D],
D [auth E]
L-PEPTIDE LINKINGC5 H11 N O2 SeMET

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.21 Å
  • R-Value Free:  0.299 (Depositor), 0.309 (DCC) 
  • R-Value Work:  0.258 (Depositor), 0.267 (DCC) 
  • R-Value Observed: 0.262 (Depositor) 
Space Group: I 41 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 256.75α = 90
b = 256.75β = 90
c = 256.75γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
SHELXDEphasing
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Danish National Research FoundationDenmarkDNRF 120
Novo Nordisk FoundationDenmarkNNF18OC0030646

Revision History  (Full details and data files)

  • Version 1.0: 2020-11-04
    Type: Initial release
  • Version 1.1: 2021-02-17
    Changes: Database references
  • Version 1.2: 2023-10-04
    Changes: Data collection, Database references
  • Version 1.3: 2023-11-15
    Changes: Data collection
  • Version 1.4: 2024-11-06
    Changes: Structure summary