6DTZ: DNA primase large subunit

Crystal structure of eukaryotic DNA primase large subunit iron-sulfur cluster domain, Y397F mutant. Determined by X-ray diffraction at 1.36 Å resolution. Released 12 Dec 2018.

Method: X-ray diffraction
Resolution: 1.36 Å
Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Chains: 1
Atoms: 1,746
Mol. weight: 24.05 kDa
Ligands: MRD, SF4
Released: 12 Dec 2018

Explore 6DTZ in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6DTZ contains 16 α-helices and 0 β-strands across 1 chain. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 16 helices, 0 β-strands

Element	Residues	Length
α-helix	323-325	3
α-helix	327-330	4
α-helix	335-347	13
α-helix	352-364	13
α-helix	369-381	13
α-helix	382-384	3
α-helix	388-394	7
α-helix	396-402	7
α-helix	413-415	3
α-helix	417-422	6
α-helix	424-426	3
α-helix	435-438	4
α-helix	441-450	10
α-helix	455-466	12
α-helix	470-480	11
α-helix	500-509	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
DNA primase large subunit	A	protein	201	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P20457 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>6DTZ_1 DNA primase large subunit (chains A)
GPGSDDEINAQSVWSEEISSNYPLCIKNLMEGLKKNHHLRYYGRQQLSLFLKGIGLSADE
ALKFWSEAFTRNGNMTMEKFNKEYRFSFRHNYGLEGNRINYKPWDCHTILSKPRPGRGDY
HGCPFRDWSHERLSAELRSMKLTQAQIISVLDSCQKGEYTIACTKVFEMTHNSASADLEI
GEQTHIAHPNLYFERSRQLQK

Ligands and cofactors

ID	Name	Formula	Copies
MRD	(4R)-2-methylpentane-2,4-diol	C6 H14 O2	1
SF4	Iron/sulfur cluster	Fe4 S4	1

Water and common crystallization additives (MPD) are not listed.

Primary citation

Yeast require redox switching in DNA primase. O'Brien, E., Salay, L.E., Epum, E.A. et al. Proc Natl Acad Sci U S A (2018) 115:13186-13191. DOI 10.1073/pnas.1810715115 · PubMed

Other PDB entries of the same protein (UniProt P20457 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6DTV 1.12 Å, Crystal structure of eukaryotic DNA primase large subunit iron-sulfur cluster domain…
7TL2 1.53 Å, Crystal Structure of Yeast p58C Multi-Tyrosine Mutant 5YF412
3LGB 1.54 Å, Crystal Structure of the Fe-S Domain of the yeast DNA primase
7TL4 1.8 Å, Crystal Structure of Yeast p58C Multi-Tyrosine Mutant 6YF
6DU0 1.82 Å, Crystal structure of eukaryotic DNA primase large subunit iron-sulfur cluster domain…
7TL3 2.07 Å, Crystal Structure of Yeast p58C Multi-Tyrosine Mutant 5YF431
8B9A 3.5 Å, S. cerevisiae replisome + Ctf4, bound by pol alpha primase. Complex engaged with a fork…
8B9B 3.5 Å, S. cerevisiae replisome + Ctf4, bound by pol alpha. Complex engaged with a fork DNA…
8FOK 3.56 Å, Cryo-EM structure of S. cerevisiae DNA polymerase alpha-primase complex in the DNA…
8FOC 3.7 Å, Cryo-EM structure of S. cerevisiae DNA polymerase alpha-primase in Apo state…
8FOD 3.8 Å, Cryo-EM structure of S. cerevisiae DNA polymerase alpha-primase complex in Apo state…
8B9C 4.6 Å, S. cerevisiae pol alpha - replisome complex

Browse structure collections

About this viewer

MolViewer shows 6DTZ directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.