8XAY

Cryo-EM structure of an anti-phage defense complex bound to ATPrS and DNA


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.81 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Molecular and structural basis of an ATPase-nuclease dual-enzyme anti-phage defense complex.

An, Q.Wang, Y.Tian, Z.Han, J.Li, J.Liao, F.Yu, F.Zhao, H.Wen, Y.Zhang, H.Deng, Z.

(2024) Cell Res 

  • DOI: https://doi.org/10.1038/s41422-024-00981-w
  • Primary Citation of Related Structures:  
    8XAU, 8XAV, 8XAW, 8XAX, 8XAY

  • PubMed Abstract: 

    Coupling distinct enzymatic effectors emerges as an efficient strategy for defense against phage infection in bacterial immune responses, such as the widely studied nuclease and cyclase activities in the type III CRISPR-Cas system. However, concerted enzymatic activities in other bacterial defense systems are poorly understood. Here, we biochemically and structurally characterize a two-component defense system DUF4297-HerA, demonstrating that DUF4297-HerA confers resistance against phage infection by cooperatively cleaving dsDNA and hydrolyzing ATP. DUF4297 alone forms a dimer, and HerA alone exists as a nonplanar split spiral hexamer, both of which exhibit extremely low enzymatic activity. Interestingly, DUF4297 and HerA assemble into an approximately 1 MDa supramolecular complex, where two layers of DUF4297 (6 DUF4297 molecules per layer) linked via inter-layer dimerization of neighboring DUF4297 molecules are stacked on top of the HerA hexamer. Importantly, the complex assembly promotes dimerization of DUF4297 molecules in the upper layer and enables a transition of HerA from a nonplanar hexamer to a planar hexamer, thus activating their respective enzymatic activities to abrogate phage infection. Together, our findings not only characterize a novel dual-enzyme anti-phage defense system, but also reveal a unique activation mechanism by cooperative complex assembly in bacterial immunity.


  • Organizational Affiliation

    Key Laboratory of Virology and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei, China.


Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ATP-binding protein
A, B, C, D, E
A, B, C, D, E, F
571Escherichia coliMutation(s): 0 
Gene Names: CG692_10950
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
DUF4297
G, H, I, J, K
G, H, I, J, K, L, M, N, O, P, Q, R
394Escherichia coliMutation(s): 0 
Gene Names: CG692_10945
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Find similar nucleic acids by: 3D Structure
Entity ID: 3
MoleculeChains LengthOrganismImage
S20DNA359Escherichia coli
Sequence Annotations
Expand
  • Reference Sequence
Find similar nucleic acids by: 3D Structure
Entity ID: 4
MoleculeChains LengthOrganismImage
S20DNA459Escherichia coli
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
AGS (Subject of Investigation/LOI)
Query on AGS

Download Ideal Coordinates CCD File 
AA [auth D],
U [auth A],
W [auth B],
Y [auth C]
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
C10 H16 N5 O12 P3 S
NLTUCYMLOPLUHL-KQYNXXCUSA-N
ADP (Subject of Investigation/LOI)
Query on ADP

Download Ideal Coordinates CCD File 
CA [auth E],
EA [auth F]
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
MG (Subject of Investigation/LOI)
Query on MG

Download Ideal Coordinates CCD File 
BA [auth D]
DA [auth E]
FA [auth F]
V [auth A]
X [auth B]
BA [auth D],
DA [auth E],
FA [auth F],
V [auth A],
X [auth B],
Z [auth C]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.81 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2024-06-05
    Type: Initial release
  • Version 1.1: 2024-07-10
    Changes: Data collection, Database references