› 6lwr

X-ray diffraction
2.9Å resolution

Crystal structure of human NEIL1(K242) bound to duplex DNA containing a cleaved C:T mismatch

Released:
DOI: 10.2210/pdb6lwr/pdb
PDB entry 6lwr coloured by chain, front view.
PDB entry 6lwr coloured by chain, side view.
PDB entry 6lwr coloured by chain, top view.
Source organisms:
Primary publication:
DNA repair glycosylase hNEIL1 triages damaged bases via competing interaction modes.
Liu M, Zhang J, Zhu C, Zhang X, Xiao W, Yan Y, Liu L, Zeng H, Gao YQ, Yi C
Nat Commun 12 4108 (2021)
PMID: 34226550

Function and Biology Details

Reaction catalysed: 
The C-O-P bond 3' to the apurinic or apyrimidinic site in DNA is broken by a beta-elimination reaction, leaving a 3'-terminal unsaturated sugar and a product with a terminal 5'-phosphate
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-120248 (preferred)
Entry contents:
1 distinct polypeptide molecule
3 distinct DNA molecules
Macromolecules (4 distinct):
Endonuclease 8-like 1 Chains: A, E
Molecule details ›
Chains: A, E
Length: 295 amino acids
Theoretical weight: 33.3 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q96FI4 (Residues: 1-295; Coverage: 76%)
Gene name: NEIL1
Sequence domains:
DNA (5'-D(*CP*GP*TP*CP*CP*(PDA))-3') Chains: B, F
Molecule details ›
Chains: B, F
Length: 6 nucleotides
Theoretical weight: 1.85 KDa
Source organism: Escherichia coli
Expression system: Not provided
DNA (5'-D(*CP*GP*TP*CP*CP*(PDA))-3') Chains: C, G
Molecule details ›
Chains: C, G
Length: 6 nucleotides
Theoretical weight: 1.78 KDa
Source organism: Escherichia coli
Expression system: Not provided
DNA (5'-D(*TP*AP*GP*AP*CP*CP*TP*GP*GP*AP*CP*GP*G)-3') Chains: D, H
Molecule details ›
Chains: D, H
Length: 13 nucleotides
Theoretical weight: 4.02 KDa
Source organism: Escherichia coli
Expression system: Not provided

Ligands and Environments

No bound ligands
1 modified residue:
Ligand AD2 2 x AD2

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRF BEAMLINE BL19U1
Spacegroup: P21212
Unit cell:
a: 88.992Å b: 143.573Å c: 71.165Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.21 0.208 0.248
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

4 citation in other articles

NEIL1 Recoding due to RNA Editing Impacts Lesion-Specific Recognition and Excision.
Lotsof et al. (2022)
3 more