› 5dv4

X-ray diffraction
1.8Å resolution

Crystal structure of human CNOT6L in complex with neomycin

Released:
DOI: 10.2210/pdb5dv4/pdb
PDB entry 5dv4 coloured by chain, front view.
PDB entry 5dv4 coloured by chain, side view.
PDB entry 5dv4 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structural basis for inhibition of the deadenylase activity of human CNOT6L.
Zhang Q, Yan D, Guo E, Ding B, Yang W, Liu R, Yamamoto T, Bartlam M
FEBS Lett 590 1270-9 (2016)
PMID: 27013054

Function and Biology Details

Reaction catalysed: 
Exonucleolytic cleavage of poly(A) to 5'-AMP
Biochemical function:
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-188618 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
CCR4-NOT transcription complex subunit 6-like Chain: A
Molecule details ›
Chain: A
Length: 398 amino acids
Theoretical weight: 45.14 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q96LI5 (Residues: 158-555; Coverage: 72%)
Gene names: CCR4B, CNOT6L
Sequence domains: Endonuclease/Exonuclease/phosphatase family
Structure domains: Endonuclease/exonuclease/phosphatase

Ligands and Environments

2 bound ligands:
Ligand NMY 1 x NMY
Ligand SO4 2 x SO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: PHOTON FACTORY BEAMLINE BL-5A
Spacegroup: P3221
Unit cell:
a: 77.388Å b: 77.388Å c: 167.188Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.191 0.19 0.216
Expression system: Escherichia coli

Quick links

Citations

4 citation in other articles

Deadenylase-dependent mRNA decay of GDF15 and FGF21 orchestrates food intake and energy expenditure.
Katsumura et al. (2022)
3 more