3LGB: Fe-S Domain of the yeast DNA primase

Crystal Structure of the Fe-S Domain of the yeast DNA primase. Determined by X-ray diffraction at 1.54 Å resolution. Released 21 Apr 2010.

Method: X-ray diffraction
Resolution: 1.54 Å
Organism: Saccharomyces cerevisiae
Chains: 2
Atoms: 3,704
Mol. weight: 47.29 kDa
Ligands: SF4, ZN
Released: 21 Apr 2010

Explore 3LGB in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3LGB contains 31 α-helices and 0 β-strands across 2 chains. 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: 15 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	369-379	11
α-helix	388-394	7
α-helix	396-402	7
α-helix	412-415	4
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	470-481	12
α-helix	500-510	11

Chain B: 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	369-379	11
α-helix	388-390	3
α-helix	391-395	5
α-helix	396-402	7
α-helix	412-415	4
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	470-482	13
α-helix	500-509	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
DNA primase large subunit	A, B	protein	194	Saccharomyces cerevisiae	P20457 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>3LGB_1 DNA primase large subunit (chains A, B)
SDEINAQSVWSEEISSNYPLCIKNLMEGLKKNHHLRYYGRQQLSLFLKGIGLSADEALKF
WSEAFTNMTMEKFNKEYRYSFRHNYGLEGNRINYKPWDCHTILSKPRPGRGDYHGCPFRD
WSHERLSAELRSMKLTQAQIISVLDSCQKGEYTIACTKVFEMTHNSASADLEIGEQTHIA
HPNLYFERSRQLQK

Ligands and cofactors

ID	Name	Formula	Copies
SF4	Iron/sulfur cluster	Fe4 S4	2
ZN	Zinc ion	Zn	2

Water and common crystallization additives (EPE, GOL) are not listed.

Primary citation

Shared Active Site Architecture between the Large Subunit of Eukaryotic Primase and DNA Photolyase. Sauguet, L., Klinge, S., Perera, R.L. et al. PLoS One (2010) 5:10083-10083. DOI 10.1371/journal.pone.0010083 · 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…
6DTZ 1.36 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
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

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