8J4U | pdb_00008j4u

Structure of HerA-Sir2 complex from Escherichia coli Nezha system


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.97 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 8J4U

This is version 1.1 of the entry. See complete history

Literature

Multiple enzymatic activities of a Sir2-HerA system cooperate for anti-phage defense.

Tang, D.Chen, Y.Chen, H.Jia, T.Chen, Q.Yu, Y.

(2023) Mol Cell 83: 4600-4613.e6

  • DOI: https://doi.org/10.1016/j.molcel.2023.11.010
  • Primary Citation Related Structures: 
    8J4U

  • PubMed Abstract: 

    In response to the persistent exposure to phage infection, bacteria have evolved diverse antiviral defense mechanisms. In this study, we report a bacterial two-component defense system consisting of a Sir2 NADase and a HerA helicase. Cryo-electron microscopy reveals that Sir2 and HerA assemble into a ∼1 MDa supramolecular octadecamer. Unexpectedly, this complex exhibits various enzymatic activities, including ATPase, NADase, helicase, and nuclease, which work together in a sophisticated manner to fulfill the antiphage function. Therefore, we name this defense system "Nezha" after a divine warrior in Chinese mythology who employs multiple weapons to defeat enemies. Our findings demonstrate that Nezha could sense phage infections, self-activate to arrest cell growth, eliminate phage genomes, and subsequently deactivate to allow for cell recovery. Collectively, Nezha represents a paradigm of sophisticated and multifaceted strategies bacteria use to defend against viral infections.


  • Organizational Affiliation
    • Department of Urology, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China.

Macromolecule Content 

  • Total Structure Weight: 981.76 kDa 
  • Atom Count: 65,570 
  • Modeled Residue Count: 8,154 
  • Deposited Residue Count: 8,640 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
SIR2-like domain-containing protein
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L
415Escherichia coliMutation(s): 0 
Gene Names: ERS139208_00135
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Nucleoside triphosphate hydrolase
M, N, O, P, Q
M, N, O, P, Q, R
610Escherichia coliMutation(s): 0 
Gene Names: ERS139208_00134

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
AR6

Query on AR6



Download:Ideal Coordinates CCD File
AA [auth I]
BA [auth J]
CA [auth K]
DA [auth L]
S [auth A]
AA [auth I],
BA [auth J],
CA [auth K],
DA [auth L],
S [auth A],
T [auth B],
U [auth C],
V [auth D],
W [auth E],
X [auth F],
Y [auth G],
Z [auth H]
[(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL[HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] HYDROGEN PHOSPHATE
C15 H23 N5 O14 P2
SRNWOUGRCWSEMX-ZQSHOCFMSA-N
AGS

Query on AGS



Download:Ideal Coordinates CCD File
EA [auth M],
FA [auth N],
HA [auth O],
IA [auth P],
JA [auth Q]
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
C10 H16 N5 O12 P3 S
NLTUCYMLOPLUHL-KQYNXXCUSA-N
MG

Query on MG



Download:Ideal Coordinates CCD File
GA [auth N]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.97 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China32270761, 31741027

Revision History  (Full details and data files)

  • Version 1.0: 2024-01-03
    Type: Initial release
  • Version 1.1: 2025-06-18
    Changes: Data collection, Derived calculations, Structure summary