6P8V | pdb_00006p8v

Structure of E. coli MS115-1 HORMA:CdnC:Trip13 complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.64 Å
  • R-Value Free: 
    0.271 (Depositor), 0.274 (DCC) 
  • R-Value Work: 
    0.233 (Depositor), 0.234 (DCC) 
  • R-Value Observed: 
    0.235 (Depositor) 

Starting Model: experimental
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This is version 1.5 of the entry. See complete history

Literature

HORMA Domain Proteins and a Trip13-like ATPase Regulate Bacterial cGAS-like Enzymes to Mediate Bacteriophage Immunity.

Ye, Q.Lau, R.K.Mathews, I.T.Birkholz, E.A.Watrous, J.D.Azimi, C.S.Pogliano, J.Jain, M.Corbett, K.D.

(2020) Mol Cell 77: 709

  • DOI: https://doi.org/10.1016/j.molcel.2019.12.009
  • Primary Citation Related Structures: 
    6P80, 6P82, 6P8J, 6P8O, 6P8P, 6P8R, 6P8S, 6P8U, 6P8V, 6PB3, 6U7B

  • PubMed Abstract: 

    Bacteria are continually challenged by foreign invaders, including bacteriophages, and have evolved a variety of defenses against these invaders. Here, we describe the structural and biochemical mechanisms of a bacteriophage immunity pathway found in a broad array of bacteria, including E. coli and Pseudomonas aeruginosa. This pathway uses eukaryotic-like HORMA domain proteins that recognize specific peptides, then bind and activate a cGAS/DncV-like nucleotidyltransferase (CD-NTase) to generate a cyclic triadenylate (cAAA) second messenger; cAAA in turn activates an endonuclease effector, NucC. Signaling is attenuated by a homolog of the AAA+ ATPase Pch2/TRIP13, which binds and disassembles the active HORMA-CD-NTase complex. When expressed in non-pathogenic E. coli, this pathway confers immunity against bacteriophage λ through an abortive infection mechanism. Our findings reveal the molecular mechanisms of a bacterial defense pathway integrating a cGAS-like nucleotidyltransferase with HORMA domain proteins for threat sensing through protein detection and negative regulation by a Trip13 ATPase.


  • Organizational Affiliation
    • Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA.

Macromolecule Content 

  • Total Structure Weight: 266.28 kDa 
  • Atom Count: 17,816 
  • Modeled Residue Count: 2,265 
  • Deposited Residue Count: 2,361 
  • Unique protein chains: 3

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
ATPase, AAA family
A, B, C, D, E
A, B, C, D, E, F
311Escherichia coli MS 115-1Mutation(s): 1 
Gene Names: HMPREF9540_01760
UniProt
Find proteins for D7Y2H4 (Escherichia coli (strain MS 115-1))
Explore D7Y2H4 
Go to UniProtKB:  D7Y2H4
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD7Y2H4
Sequence Annotations
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
E. coli MS115-1 CdnC321Escherichia coli MS 115-1Mutation(s): 0 
Gene Names: HMPREF9540_01758
EC: 2.7.7.85 (UniProt), 2.7.7 (UniProt)
UniProt
Find proteins for D7Y2H2 (Escherichia coli (strain MS 115-1))
Explore D7Y2H2 
Go to UniProtKB:  D7Y2H2
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD7Y2H2
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
E. coli MS115-1 HORMA174Escherichia coliMutation(s): 0 
Gene Names: BHS87_27760CG706_08820
UniProt
Find proteins for D7Y2H3 (Escherichia coli (strain MS 115-1))
Explore D7Y2H3 
Go to UniProtKB:  D7Y2H3
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD7Y2H3
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.64 Å
  • R-Value Free:  0.271 (Depositor), 0.274 (DCC) 
  • R-Value Work:  0.233 (Depositor), 0.234 (DCC) 
  • R-Value Observed: 0.235 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 89.789α = 90
b = 138.516β = 98.18
c = 100.212γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-12-25
    Type: Initial release
  • Version 1.1: 2020-01-22
    Changes: Database references, Structure summary
  • Version 1.2: 2020-03-04
    Changes: Database references
  • Version 1.3: 2023-10-11
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.4: 2023-11-15
    Changes: Data collection, Database references
  • Version 1.5: 2024-11-20
    Changes: Structure summary