6U7B

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.09 Å
  • R-Value Free: 
    0.233 (Depositor), 0.230 (DCC) 
  • R-Value Work: 
    0.205 (Depositor), 0.200 (DCC) 
  • R-Value Observed: 
    0.206 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted AMPClick on this verticalbar to view details

This is version 1.3 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 of 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.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
E. coli MS115-1 CdnC
A, C
321Escherichia 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
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
bacHORMA_1 domain-containing protein
B, D
179Escherichia coliMutation(s): 0 
Gene Names: BHS87_27760EPS97_06770
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
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
AMP
Query on AMP

Download Ideal Coordinates CCD File 
K [auth C]ADENOSINE MONOPHOSPHATE
C10 H14 N5 O7 P
UDMBCSSLTHHNCD-KQYNXXCUSA-N
ACT
Query on ACT

Download Ideal Coordinates CCD File 
G [auth B],
H [auth B],
I [auth B],
M [auth D],
N [auth D]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
CL
Query on CL

Download Ideal Coordinates CCD File 
F [auth A],
L [auth C]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG
Query on MG

Download Ideal Coordinates CCD File 
E [auth A],
J [auth C]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.09 Å
  • R-Value Free:  0.233 (Depositor), 0.230 (DCC) 
  • R-Value Work:  0.205 (Depositor), 0.200 (DCC) 
  • R-Value Observed: 0.206 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 52.286α = 90
b = 142.897β = 90
c = 151.157γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted AMPClick on this verticalbar to view details

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
  • Version 1.2: 2020-03-04
    Changes: Database references
  • Version 1.3: 2023-10-11
    Changes: Data collection, Database references, Derived calculations, Refinement description