9H9V | pdb_00009h9v

BabyBass soluble domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.42 Å
  • R-Value Free: 
    0.327 (Depositor), 0.318 (DCC) 
  • R-Value Work: 
    0.264 (Depositor), 0.255 (DCC) 
  • R-Value Observed: 
    0.267 (Depositor) 

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


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Literature

Characterization of an amyloid-based antiphage defence system in Escherichia coli.

Ibarlosa, L.Dheur, S.Sanchez, C.Deb, S.Granger-Farbos, A.Coustou, V.Berbon, M.Massoni-Laporte, A.Salin, B.Blancard, C.Saragaglia, C.Tene, X.M.Dufour, N.Rossier, O.Habenstein, B.Debarbieux, L.Kauffmann, B.Loquet, A.Saupe, S.J.

(2025) Nat Microbiol 10: 2168-2178

  • DOI: https://doi.org/10.1038/s41564-025-02074-9
  • Primary Citation of Related Structures:  
    9H9V

  • PubMed Abstract: 

    Amyloids are β-sheet-rich protein polymers that can cause disease but also serve functional purposes in cells. In animals and fungi, functional amyloids have a role in regulated cell death as molecular switches activating key cell death effectors. Here we describe an amyloid-based abortive infection antiphage defence system in Escherichia coli. This system leads to death of phage-infected cells and involves two proteins, Bab and Agp, which share a common amyloid motif and are encoded by adjacent genes. Following infection, Agp activates Bab through amyloid signalling. Activation of Bab then causes membrane alterations and cell death. We determined the structure of the cell death execution domain of Bab, which is distantly related to pore-forming domains found in fungi, animals and plants. We show that Bab and HET-S, a fungal amyloid-controlled regulated cell death execution protein from Podospora anserina, are functionally interchangeable. These findings show that amyloid-mediated immune signalling is conserved across kingdoms.


  • Organizational Affiliation
    • IBGC, UMR 5095, CNRS-Université de Bordeaux, Bordeaux, France.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Babybass85Escherichia coliMutation(s): 0 
Gene Names: CTR35_000088J0541_000148
UniProt
Find proteins for A0A3L9BKH8 (Escherichia coli)
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Go to UniProtKB:  A0A3L9BKH8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A3L9BKH8
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Babybass
B, E
82Escherichia coliMutation(s): 0 
Gene Names: CTR35_000088J0541_000148
UniProt
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Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A3L9BKH8
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Babybass84Escherichia coliMutation(s): 0 
Gene Names: CTR35_000088J0541_000148
UniProt
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Go to UniProtKB:  A0A3L9BKH8
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UniProt GroupA0A3L9BKH8
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Babybass85Escherichia coliMutation(s): 0 
Gene Names: CTR35_000088J0541_000148
UniProt
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Go to UniProtKB:  A0A3L9BKH8
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Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A3L9BKH8
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Babybass
F, H
83Escherichia coliMutation(s): 0 
Gene Names: CTR35_000088J0541_000148
UniProt
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Go to UniProtKB:  A0A3L9BKH8
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UniProt GroupA0A3L9BKH8
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  • Reference Sequence
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Babybass84Escherichia coliMutation(s): 0 
Gene Names: CTR35_000088J0541_000148
UniProt
Find proteins for A0A3L9BKH8 (Escherichia coli)
Explore A0A3L9BKH8 
Go to UniProtKB:  A0A3L9BKH8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A3L9BKH8
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.42 Å
  • R-Value Free:  0.327 (Depositor), 0.318 (DCC) 
  • R-Value Work:  0.264 (Depositor), 0.255 (DCC) 
  • R-Value Observed: 0.267 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 108.041α = 90
b = 119.621β = 92.52
c = 64.172γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
CrysalisProdata reduction
CrysalisProdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2025-10-08
    Type: Initial release