8OLJ

Crystal structure of Archaeoglobus fulgidus AfAgo-N protein representing N-L1-L2 domains


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.178 
  • R-Value Work: 0.145 
  • R-Value Observed: 0.148 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

The missing part: the Archaeoglobus fulgidus Argonaute forms a functional heterodimer with an N-L1-L2 domain protein.

Manakova, E.Golovinas, E.Poceviciute, R.Sasnauskas, G.Silanskas, A.Rutkauskas, D.Jankunec, M.Zagorskaite, E.Jurgelaitis, E.Grybauskas, A.Venclovas, C.Zaremba, M.

(2024) Nucleic Acids Res 52: 2530-2545

  • DOI: https://doi.org/10.1093/nar/gkad1241
  • Primary Citation of Related Structures:  
    8OK9, 8OLD, 8OLJ, 8PVV, 8QG0

  • PubMed Abstract: 

    Argonaute (Ago) proteins are present in all three domains of life (bacteria, archaea and eukaryotes). They use small (15-30 nucleotides) oligonucleotide guides to bind complementary nucleic acid targets and are responsible for gene expression regulation, mobile genome element silencing, and defence against viruses or plasmids. According to their domain organization, Agos are divided into long and short Agos. Long Agos found in prokaryotes (long-A and long-B pAgos) and eukaryotes (eAgos) comprise four major functional domains (N, PAZ, MID and PIWI) and two structural linker domains L1 and L2. The majority (∼60%) of pAgos are short pAgos, containing only the MID and inactive PIWI domains. Here we focus on the prokaryotic Argonaute AfAgo from Archaeoglobus fulgidus DSM4304. Although phylogenetically classified as a long-B pAgo, AfAgo contains only MID and catalytically inactive PIWI domains, akin to short pAgos. We show that AfAgo forms a heterodimeric complex with a protein encoded upstream in the same operon, which is a structural equivalent of the N-L1-L2 domains of long pAgos. This complex, structurally equivalent to a long PAZ-less pAgo, outperforms standalone AfAgo in guide RNA-mediated target DNA binding. Our findings provide a missing piece to one of the first and the most studied pAgos.


  • Organizational Affiliation

    Institute of Biotechnology, Life Sciences Center, Vilnius University, Sauletekio av. 7, LT-10257, Vilnius, Lithuania.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Archaeoglobus fulgidus AfAgo-N protein representing N-L1-L2 domainsA [auth B]264Archaeoglobus fulgidus DSM 8774Mutation(s): 0 
Gene Names: AFULGI_00014290
UniProt
Find proteins for A0A075WKW4 (Archaeoglobus fulgidus DSM 8774)
Explore A0A075WKW4 
Go to UniProtKB:  A0A075WKW4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A075WKW4
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
TRS
Query on TRS

Download Ideal Coordinates CCD File 
S [auth B]2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
GOL
Query on GOL

Download Ideal Coordinates CCD File 
B,
C [auth B],
D [auth B],
E [auth B],
F [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
IPA
Query on IPA

Download Ideal Coordinates CCD File 
G [auth B]
H [auth B]
I [auth B]
J [auth B]
K [auth B]
G [auth B],
H [auth B],
I [auth B],
J [auth B],
K [auth B],
L [auth B],
M [auth B],
N [auth B],
O [auth B]
ISOPROPYL ALCOHOL
C3 H8 O
KFZMGEQAYNKOFK-UHFFFAOYSA-N
ACY
Query on ACY

Download Ideal Coordinates CCD File 
T [auth B]ACETIC ACID
C2 H4 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-N
K
Query on K

Download Ideal Coordinates CCD File 
P [auth B],
Q [auth B],
R [auth B]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.178 
  • R-Value Work: 0.145 
  • R-Value Observed: 0.148 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 75.264α = 90
b = 75.264β = 90
c = 94.722γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Research Council of LithuaniaLithuaniaS-MIP-20-37
iNEXTEuropean UnionH2020 Grant # 653706

Revision History  (Full details and data files)

  • Version 1.0: 2024-01-24
    Type: Initial release
  • Version 1.1: 2024-03-27
    Changes: Database references