› 5z9x

X-ray diffraction
2.8Å resolution

Arabidopsis SMALL RNA DEGRADING NUCLEASE 1 in complex with an RNA substrate

Released:
DOI: 10.2210/pdb5z9x/pdb
PDB entry 5z9x coloured by chain, front view.
PDB entry 5z9x coloured by chain, side view.
PDB entry 5z9x coloured by chain, top view.
Source organism: Arabidopsis thaliana
Primary publication:
Structural and biochemical insights into small RNA 3' end trimming by Arabidopsis SDN1.
Chen J, Liu L, You C, Gu J, Ruan W, Zhang L, Gan J, Cao C, Huang Y, Chen X, Ma J
Nat Commun 9 3585 (2018)
PMID: 30181559

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-107161 (preferred)
Entry contents:
1 distinct polypeptide molecule
1 distinct RNA molecule
Macromolecules (2 distinct):
Small RNA degrading nuclease 1 Chain: A
Molecule details ›
Chain: A
Length: 409 amino acids
Theoretical weight: 46.43 KDa
Source organism: Arabidopsis thaliana
Expression system: Escherichia coli
UniProt:
  • Canonical: A3KPE8 (Residues: 1-409; Coverage: 100%)
Gene names: At3g50100, F3A4.180, SDN1
Sequence domains: Exonuclease
RNA (5'-R(P*GP*CP*CP*CP*AP*UP*UP*AP*G)-3') Chain: R
Molecule details ›
Chain: R
Length: 10 nucleotides
Theoretical weight: 3.16 KDa
Source organism: Arabidopsis thaliana
Expression system: Not provided

Ligands and Environments

2 bound ligands:
Ligand SO4 2 x SO4
Ligand MG 2 x MG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRF BEAMLINE BL17B1
Spacegroup: P3121
Unit cell:
a: 87.993Å b: 87.993Å c: 178.639Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.253 0.252 0.261
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

7 review citations

Plant microRNAs: Biogenesis, Homeostasis, and Degradation.
Wang et al. (2019)
6 more

3 mentions without citation

Internal RNA 2'O-methylation in the HIV-1 genome counteracts ISG20 nuclease-mediated antiviral effect.
El Kazzi et al. (2023)
2 more