7ZPF

Three-dimensional structure of AIP56, a short-trip single chain AB toxin from Photobacterium damselae subsp. piscicida.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.54 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.240 
  • R-Value Observed: 0.242 

Starting Model: in silico
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wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Unconventional structure and mechanisms for membrane interaction and translocation of the NF-kappa B-targeting toxin AIP56.

Lisboa, J.Pereira, C.Pinto, R.D.Rodrigues, I.S.Pereira, L.M.G.Pinheiro, B.Oliveira, P.Pereira, P.J.B.Azevedo, J.E.Durand, D.Benz, R.do Vale, A.Dos Santos, N.M.S.

(2023) Nat Commun 14: 7431-7431

  • DOI: https://doi.org/10.1038/s41467-023-43054-z
  • Primary Citation of Related Structures:  
    7ZPF

  • PubMed Abstract: 

    Bacterial AB toxins are secreted key virulence factors that are internalized by target cells through receptor-mediated endocytosis, translocating their enzymatic domain to the cytosol from endosomes (short-trip) or the endoplasmic reticulum (long-trip). To accomplish this, bacterial AB toxins evolved a multidomain structure organized into either a single polypeptide chain or non-covalently associated polypeptide chains. The prototypical short-trip single-chain toxin is characterized by a receptor-binding domain that confers cellular specificity and a translocation domain responsible for pore formation whereby the catalytic domain translocates to the cytosol in an endosomal acidification-dependent way. In this work, the determination of the three-dimensional structure of AIP56 shows that, instead of a two-domain organization suggested by previous studies, AIP56 has three-domains: a non-LEE encoded effector C (NleC)-like catalytic domain associated with a small middle domain that contains the linker-peptide, followed by the receptor-binding domain. In contrast to prototypical single-chain AB toxins, AIP56 does not comprise a typical structurally complex translocation domain; instead, the elements involved in translocation are scattered across its domains. Thus, the catalytic domain contains a helical hairpin that serves as a molecular switch for triggering the conformational changes necessary for membrane insertion only upon endosomal acidification, whereas the middle and receptor-binding domains are required for pore formation.


  • Organizational Affiliation

    Fish Immunology and Vaccinology Group, IBMC-Instituto de Biologia Molecular e Celular, Universidade do Porto, 4200-135, Porto, Portugal. johnny.lisboa@i3s.up.pt.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Aip56
A, B, C, D
521Photobacterium damselae subsp. piscicidaMutation(s): 0 
Gene Names: aip56E4T25_16935
UniProt
Find proteins for Q2VL32 (Photobacterium damsela subsp. piscicida)
Explore Q2VL32 
Go to UniProtKB:  Q2VL32
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ2VL32
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download Ideal Coordinates CCD File 
G [auth A],
I [auth B],
J [auth B],
K [auth B],
L [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
E [auth A],
H [auth B],
M [auth C],
O [auth D]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
NI
Query on NI

Download Ideal Coordinates CCD File 
F [auth A],
N [auth C],
P [auth D],
Q [auth D]
NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.129α = 90
b = 193.85β = 113.24
c = 91.616γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
PHENIXrefinement
XDSdata reduction
STARANISOdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Fundacao para a Ciencia e a TecnologiaPortugal268319 - PTDC/BIA-MIC/29910/2017-029910

Revision History  (Full details and data files)

  • Version 1.0: 2023-05-10
    Type: Initial release
  • Version 1.1: 2023-05-31
    Changes: Derived calculations
  • Version 1.2: 2023-06-28
    Changes: Derived calculations
  • Version 1.3: 2023-11-29
    Changes: Data collection, Database references
  • Version 1.4: 2024-05-01
    Changes: Refinement description