› 5f0q

X-ray diffraction
2.21Å resolution

Crystal structure of C-terminal domain of the human DNA primase large subunit with bound DNA template/RNA primer

Released:
DOI: 10.2210/pdb5f0q/pdb
PDB entry 5f0q coloured by chain, front view.
PDB entry 5f0q coloured by chain, side view.
PDB entry 5f0q coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Mechanism of Concerted RNA-DNA Primer Synthesis by the Human Primosome.
Baranovskiy AG, Babayeva ND, Zhang Y, Gu J, Suwa Y, Pavlov YI, Tahirov TH
J Biol Chem 291 10006-20 (2016)
PMID: 26975377

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-118657 (preferred)
Entry contents:
1 distinct polypeptide molecule
1 distinct DNA molecule
1 distinct RNA molecule
Macromolecules (3 distinct):
DNA primase large subunit Chains: A, B
Molecule details ›
Chains: A, B
Length: 191 amino acids
Theoretical weight: 22.03 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P49643 (Residues: 266-456; Coverage: 38%)
Gene names: PRIM2, PRIM2A
Sequence domains: Eukaryotic and archaeal DNA primase, large subunit
DNA (5'-D(*GP*CP*CP*GP*CP*CP*AP*AP*CP*AP*TP*A)-3') Chains: D, F
Molecule details ›
Chains: D, F
Length: 12 nucleotides
Theoretical weight: 3.62 KDa
Source organism: Homo sapiens
Expression system: Not provided
RNA (5'-R(P*GP*GP*CP*GP*GP*C)-3') Chains: C, E
Molecule details ›
Chains: C, E
Length: 6 nucleotides
Theoretical weight: 2.11 KDa
Source organism: Homo sapiens
Expression system: Not provided

Ligands and Environments

2 bound ligands:
Ligand SF4 2 x SF4
Ligand MG 2 x MG
1 modified residue:
Ligand GTP 2 x GTP

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 24-ID-C
Spacegroup: C2221
Unit cell:
a: 122.507Å b: 126.002Å c: 83.942Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.223 0.223 0.258
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

16 review citations

Eukaryotic DNA Replication Fork.
Burgers et al. (2017)
15 more

12 mentions without citation

Elaborated Action of the Human Primosome.
Baranovskiy et al. (2017)
11 more