6DHW: Primase iron-sulfur domain

Crystal structure of primase iron-sulfur domain (266-457). Determined by X-ray diffraction at 2.01 Å resolution. Released 19 Dec 2018.

Method: X-ray diffraction
Resolution: 2.01 Å
Organism: Homo sapiens
Chains: 2
Atoms: 2,948
Mol. weight: 45.45 kDa
Ligands: SF4
Released: 19 Dec 2018

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

Secondary structure: helices and β-sheets

6DHW contains 22 α-helices and 5 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: 11 helices, 3 β-strands

Element	Residues	Length	Sheet
β-strand	271-272	2	1
α-helix	273-276	4
α-helix	277-283	7
α-helix	286-298	13
α-helix	303-316	14
β-strand	318-324	7	1
β-strand	345-351	7	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	420-432	13
α-helix	444-455	12

Chain B: 11 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	273-276	4
α-helix	277-283	7
α-helix	286-298	13
α-helix	303-316	14
β-strand	318-322	5	2
β-strand	347-351	5	2
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	420-431	12
α-helix	444-455	12

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

>6DHW_1 DNA primase large subunit (chains A, B)
GNVGKISLDQIDLLSTKSFPPCMRQLHKALRENHHLRHGGRMQYGLFLKGIGLTLEQALQ
FWKQEFIKGKMDPDKFDKGYSYNIRHSFGKEGKRTDYTPFSCLKIILSNPPSQGDYHGCP
FRHSDPELLKQKLQSYKISPGGISQILDLVKGTHYQVACQKYFEMIHNVDDCGFSLNHPN
QFFCESQRILNG

Ligands and cofactors

ID	Name	Formula	Copies
SF4	Iron/sulfur cluster	Fe4 S4	2

Water and common crystallization additives (SO4) are not listed.

Primary citation

Functional and structural similarity of human DNA primase [4Fe4S] cluster domain constructs. Holt, M.E., Salay, L.E., O'Brien, E. et al. PLoS One (2018) 13:e0209345-e0209345. DOI 10.1371/journal.pone.0209345 · 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
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)
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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