› 5ulw

X-ray diffraction
2.62Å resolution

Structure of human DNA polymerase iota bound to template 1-methyl-deoxyadenosine

Released:
DOI: 10.2210/pdb5ulw/pdb
PDB entry 5ulw coloured by chain, front view.
PDB entry 5ulw coloured by chain, side view.
PDB entry 5ulw coloured by chain, top view.
Source organisms:
Primary publication:
Mechanism of error-free DNA synthesis across N1-methyl-deoxyadenosine by human DNA polymerase-ι.
Jain R, Choudhury JR, Buku A, Johnson RE, Prakash L, Prakash S, Aggarwal AK
Sci Rep 7 43904 (2017)
PMID: 28272441

Function and Biology Details

Reaction catalysed: 
Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1)
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-119223 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
DNA polymerase iota Chain: A
Molecule details ›
Chain: A
Length: 420 amino acids
Theoretical weight: 47.03 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9UNA4 (Residues: 26-445; Coverage: 57%)
Gene names: POLI, RAD30B
Sequence domains:
Structure domains:
DNA (5'-D(*AP*GP*GP*AP*CP*CP*(DOC))-3') Chain: P
Molecule details ›
Chain: P
Length: 7 nucleotides
Theoretical weight: 2.09 KDa
Source organism: unidentified
Expression system: Not provided
DNA (5'-D(*TP*(MA7)P*GP*GP*GP*TP*CP*CP*T)-3') Chain: T
Molecule details ›
Chain: T
Length: 11 nucleotides
Theoretical weight: 3.36 KDa
Source organism: unidentified
Expression system: Not provided

Ligands and Environments

3 bound ligands:
Ligand TTP 1 x TTP
Ligand MG 1 x MG
Ligand CL 1 x CL
2 modified residues:
Ligand DOC 1 x DOC
Ligand MA7 1 x MA7

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X25
Spacegroup: P6522
Unit cell:
a: 97.918Å b: 97.918Å c: 202.473Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.207 0.204 0.248
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

1 review citation

For the Better or for the Worse? The Effect of Manganese on the Activity of Eukaryotic DNA Polymerases.
Balint et al. (2023)
2 other articles

1 mention without citation

Translesion and Repair DNA Polymerases: Diverse Structure and Mechanism.
Yang et al. (2018)