9IAB | pdb_00009iab

Structure of the Argonaute-associated Cas4 family protein 1 (ACE1) from Chroococcidiopsis thermalis (CtACE1)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.57 Å
  • R-Value Free: 
    0.199 (Depositor), 0.198 (DCC) 
  • R-Value Work: 
    0.186 (Depositor), 0.186 (DCC) 
  • R-Value Observed: 
    0.186 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 9IAB

This is version 1.2 of the entry. See complete history

Literature

Cyanobacterial Argonautes and Cas4 family nucleases cooperate to interfere with invading DNA.

Bobadilla Ugarte, P.Halter, S.Mutte, S.K.Heijstek, C.Niault, T.Terenin, I.Barendse, P.Koopal, B.Roosjen, M.Boeren, S.Hauryliuk, V.Jinek, M.Westphal, A.H.Swarts, D.C.

(2025) Mol Cell 85: 1920

  • DOI: https://doi.org/10.1016/j.molcel.2025.03.025
  • Primary Citation Related Structures: 
    9IAB, 9IAC, 9IAD

  • PubMed Abstract: 

    Prokaryotic Argonaute proteins (pAgos) from the long-A clade are stand-alone immune systems that use small interfering DNA (siDNA) guides to recognize and cleave invading plasmid and virus DNA. Certain long-A pAgos are co-encoded with accessory proteins with unknown functions. Here, we show that cyanobacterial long-A pAgos act in conjunction with Argonaute-associated Cas4 family enzyme 1 (ACE1). Structural and biochemical analyses reveal that ACE1-associated pAgos mediate siDNA-guided DNA interference, akin to stand-alone pAgos. ACE1 is structurally homologous to the nuclease domain of bacterial DNA repair complexes and acts as a single-stranded DNA endonuclease that processes siDNA guides. pAgo and ACE1 form a heterodimeric long-A pAgo-ACE1 (APACE1) complex, which modulates ACE1 activity. Although ACE1-associated pAgos alone interfere with plasmids and bacteriophages, plasmid interference is boosted when pAgo and ACE1 are co-expressed. Our study reveals that pAgo-mediated immunity is enhanced by accessory proteins and broadens our mechanistic understanding of how pAgo systems interfere with invading DNA.


  • Organizational Affiliation
    • Laboratory of Biochemistry, Wageningen University, 6708 WE Wageningen, the Netherlands.

Macromolecule Content 

  • Total Structure Weight: 64.78 kDa 
  • Atom Count: 4,840 
  • Modeled Residue Count: 532 
  • Deposited Residue Count: 546 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
PD-(D/E)XK endonuclease-like domain-containing protein
A, B
273Chroococcidiopsis thermalisMutation(s): 0 
Gene Names: Chro_5200
UniProt
Find proteins for K9U6V4 (Chroococcidiopsis thermalis (strain PCC 7203))
Explore K9U6V4 
Go to UniProtKB:  K9U6V4
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupK9U6V4
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SF4

Query on SF4



Download:Ideal Coordinates CCD File
C [auth A],
J [auth B]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
MES

Query on MES



Download:Ideal Coordinates CCD File
D [auth A],
E [auth A],
K [auth B],
L [auth B]
2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
F [auth A],
G [auth A],
H [auth A],
I [auth A],
M [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.57 Å
  • R-Value Free:  0.199 (Depositor), 0.198 (DCC) 
  • R-Value Work:  0.186 (Depositor), 0.186 (DCC) 
  • R-Value Observed: 0.186 (Depositor) 
Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 44.91α = 100.17
b = 44.95β = 92.22
c = 74.06γ = 105.87
Software Package:
Software NamePurpose
XDSdata reduction
XDSdata scaling
PHENIXrefinement
PHASERphasing
Cootmodel building

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Research Council (ERC)European UnionERC-2020-STG 948783
Netherlands Organisation for Scientific Research (NWO)Netherlands016.Veni.192.072
Consejo Nacional de Ciencia y Tecnologia (CONACYT)Mexico682509
European Molecular Biology Organization (EMBO)European UnionALTF 179-2015
European Molecular Biology Organization (EMBO)European UnionaALTF 509-2017

Revision History  (Full details and data files)

  • Version 1.0: 2025-04-23
    Type: Initial release
  • Version 1.1: 2025-05-07
    Changes: Database references
  • Version 1.2: 2025-05-28
    Changes: Database references