5F0S: DNA primase large subunit

Crystal structure of C-terminal domain of the human DNA primase large subunit with bound DNA template/RNA primer and manganese ion. Determined by X-ray diffraction at 3.0 Å resolution. Released 23 Mar 2016.

Method: X-ray diffraction
Resolution: 3.0 Å
Organism: Homo sapiens
Chains: 6
Atoms: 3,773
Mol. weight: 56.31 kDa
Ligands: SF4, MN
Released: 23 Mar 2016

Explore 5F0S in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5F0S contains 29 α-helices and 4 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, 2 β-strands

Element	Residues	Length	Sheet
α-helix	273-275	3
α-helix	276-282	7
α-helix	286-298	13
α-helix	303-316	14
α-helix	320-332	13
α-helix	338-341	4
α-helix	342-346	5
α-helix	347-352	6
β-strand	353	1	1
β-strand	361	1	1
α-helix	362-366	5
α-helix	367-372	6
α-helix	385-388	4
α-helix	391-400	10
α-helix	405-416	12
α-helix	420-431	12
α-helix	444-455	12

Chain B: 14 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	273-275	3
α-helix	276-282	7
α-helix	286-298	13
α-helix	303-315	13
α-helix	320-332	13
α-helix	338-343	6
α-helix	345-352	8
β-strand	353	1	2
β-strand	361	1	2
α-helix	362-366	5
α-helix	367-372	6
α-helix	385-388	4
α-helix	391-400	10
α-helix	405-416	12
α-helix	420-431	12
α-helix	444-454	11

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
DNA primase large subunit	A, B	protein	191	Homo sapiens	P49643 (AlphaFold model)
RNA (5'-r(pgpgpcpgpgpc)-3')	C, E	RNA	6	Homo sapiens
DNA (5'-d(gpcpcpgpcpcpapapcpaptpa)-3')	D, F	DNA	12	Homo sapiens

Sequence of entity 1 (A, B), FASTA

>5F0S_1 DNA primase large subunit (chains A, B)
GNVGKISLDQIDLLSTKSFPPCMRQLHKALRENHHLRHGGRMQYGLFLKGIGLTLEQALQ
FWKQEFIKGKMDPDKFDKGYSYNIRHSFGKEGKRTDYTPFSCLKIILSNPPSQGDYHGCP
FRHSDPELLKQKLQSYKISPGGISQILDLVKGTHYQVACQKYFEMIHNVDDCGFSLNHPN
QFFCESQRILN

Sequence of entity 2 (C, E), FASTA

>5F0S_2 RNA (5'-R(P*GP*GP*CP*GP*GP*C)-3') (chains C, E)
GGCGGC

Sequence of entity 3 (D, F), FASTA

>5F0S_3 DNA (5'-D(*GP*CP*CP*GP*CP*CP*AP*AP*CP*AP*TP*A)-3') (chains D, F)
GCCGCCAACATA

Ligands and cofactors

ID	Name	Formula	Copies
SF4	Iron/sulfur cluster	Fe4 S4	2
MN	Manganese (II) ion	Mn	2

Primary citation

Mechanism of Concerted RNA-DNA Primer Synthesis by the Human Primosome. Baranovskiy, A.G., Babayeva, N.D., Zhang, Y. et al. J Biol Chem (2016) 291:10006-10020. DOI 10.1074/jbc.M116.717405 · PubMed

Other PDB entries of the same protein (UniProt P49643 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3L9Q 1.7 Å, Crystal structure of human polymerase alpha-primase p58 iron-sulfur cluster domain
5I7M 1.93 Å, Crystal structure of Y345F mutant of human primase p58 iron-sulfur cluster domain
6DHW 2.01 Å, Crystal structure of primase iron-sulfur domain (266-457)
5F0Q 2.21 Å, Crystal structure of C-terminal domain of the human DNA primase large subunit with bound…
5DQO 2.3 Å, Crystal structure of Y347F mutant of human primase p58 iron-sulfur cluster domain
3Q36 2.5 Å, Crystal structure of the 4Fe-4S cluster domain of human DNA primase large subunit
4RR2 2.65 Å, Crystal structure of human primase
4BPU 2.7 Å, Crystal structure of human primase in heterodimeric form, comprising PriS and truncated…
8VY3 2.98 Å, Human DNA polymerase alpha/primase - AavLEA1 (1:40 molar ratio)
4BPW 3.0 Å, Crystal structure of human primase bound to UTP
8QJ7 3.07 Å, Cryo-EM structure of human DNA polymerase alpha-primase in pre-initiation stage 1
8D96 3.35 Å, Human DNA polymerase alpha/primase elongation complex I bound to primer/template

Browse structure collections

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