3Q36: DNA primase large subunit

Crystal structure of the 4Fe-4S cluster domain of human DNA primase large subunit. Determined by X-ray diffraction at 2.5 Å resolution. Released 13 Apr 2011.

Method: X-ray diffraction
Resolution: 2.5 Å
Organism: Homo sapiens
Chains: 2
Atoms: 2,944
Mol. weight: 44.93 kDa
Ligands: FE, SF4
Released: 13 Apr 2011

Explore 3Q36 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3Q36 contains 27 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: 14 helices, 0 β-strands

Element	Residues	Length
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	338-344	7
α-helix	346-352	7
α-helix	363-366	4
α-helix	367-372	6
α-helix	385-388	4
α-helix	391-400	10
α-helix	405-416	12
α-helix	420-432	13
α-helix	444-452	9

Chain B: 13 helices, 0 β-strands

Element	Residues	Length
α-helix	276-282	7
α-helix	286-298	13
α-helix	303-315	13
α-helix	320-331	12
α-helix	338-341	4
α-helix	342-346	5
α-helix	347-352	6
α-helix	367-372	6
α-helix	385-388	4
α-helix	391-400	10
α-helix	405-416	12
α-helix	420-432	13
α-helix	444-454	11

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
DNA primase large subunit	A, B	protein	192	Homo sapiens	P49643 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>3Q36_1 DNA primase large subunit (chains A, B)
GNVGKISLDQIDLLSTKSFPPCMRQLHKALRENHHLRHGGRMQYGLFLKGIGLTLEQALQ
FWKQEFIKGKMDPDKFDKGYSYNIRHSFGKEGKRTDYTPFSCLKIILSNPPSQGDYHGCP
FRHSDPELLKQKLQSYKISPGGISQILDLVKGTHYQVACQKYFEMIHNVDDCGFSLNHPN
QFFCESQRILNG

Ligands and cofactors

ID	Name	Formula	Copies
FE	FE (III) ion	Fe	1
SF4	Iron/sulfur cluster	Fe4 S4	2

Primary citation

Crystal structure of the C-terminal domain of human DNA primase large subunit: Implications for the mechanism of the primase - polymerase alpha switch. Agarkar, V.B., Babayeva, N.D., Pavlov, Y.I. et al. Cell Cycle (2011) 10:926-931. 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
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)
5F0S 3.0 Å, Crystal structure of C-terminal domain of the human DNA primase large subunit with bound…
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

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