› 5v04

X-ray diffraction
2.65Å resolution

Crystal structure of human exonuclease 1 Exo1 (WT) in complex with 5' recessed-end DNA (rII)

Released:
DOI: 10.2210/pdb5v04/pdb
PDB entry 5v04 coloured by chain, front view.
PDB entry 5v04 coloured by chain, side view.
PDB entry 5v04 coloured by chain, top view.
Source organisms:
Primary publication:
Interplay of catalysis, fidelity, threading, and processivity in the exo- and endonucleolytic reactions of human exonuclease I.
Shi Y, Hellinga HW, Beese LS
Proc Natl Acad Sci U S A 114 6010-6015 (2017)
PMID: 28533382

Function and Biology Details

Biochemical function:
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-119244 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
Exonuclease 1 Chain: Z
Molecule details ›
Chain: Z
Length: 358 amino acids
Theoretical weight: 40.35 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9UQ84 (Residues: 1-352; Coverage: 42%)
Gene names: EXO1, EXOI, HEX1
Sequence domains:
Structure domains:
DNA (5'-D(*CP*GP*CP*TP*AP*GP*TP*CP*GP*AP*CP*AP*T)-3') Chain: A
Molecule details ›
Chain: A
Length: 13 nucleotides
Theoretical weight: 3.95 KDa
Source organism: synthetic construct
Expression system: Not provided
DNA (5'-D(P*TP*CP*GP*AP*CP*TP*AP*GP*CP*G)-3') Chain: B
Molecule details ›
Chain: B
Length: 10 nucleotides
Theoretical weight: 3.05 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

1 bound ligand:
Ligand NA 1 x NA
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 22-ID
Spacegroup: P43212
Unit cell:
a: 73.815Å b: 73.815Å c: 180.947Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.231 0.229 0.256
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

1 review citation

Implementing fluorescence enhancement, quenching, and FRET for investigating flap endonuclease 1 enzymatic reaction at the single-molecule level.
Sobhy et al. (2021)
21 other articles

2 mentions without citation

Interplay of catalysis, fidelity, threading, and processivity in the exo- and endonucleolytic reactions of human exonuclease I.
Shi et al. (2017)
1 more