4MM2: Yeast primase catalytic subunit

Crystal structure of yeast primase catalytic subunit. Determined by X-ray diffraction at 1.6 Å resolution. Released 10 Sept 2014.

Method: X-ray diffraction
Resolution: 1.6 Å
Organism: Saccharomyces cerevisiae
Chains: 2
Atoms: 6,980
Mol. weight: 97.84 kDa
Ligands: CD, CIT
Released: 10 Sept 2014

Explore 4MM2 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4MM2 contains 51 α-helices and 30 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: 26 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	9-11	3
α-helix	12-21	10
α-helix	25-33	9
β-strand	39	1	1
α-helix	40-43	4
β-strand	45-50	6	2
β-strand	56-60	5	2
α-helix	65-75	11
β-strand	79-86	8	2
α-helix	90-92	3
β-strand	103-105	3	2
β-strand	108-113	6	3
α-helix	114-117	4
α-helix	131-146	16
α-helix	147-152	6
β-strand	157-161	5	3
β-strand	166-171	6	3
α-helix	174-177	4
α-helix	181-191	11
α-helix	211-224	14
α-helix	225-232	8
α-helix	238-244	7
α-helix	246-248	3
α-helix	252-264	13
α-helix	270-285	16
α-helix	290-309	20
β-strand	313	1	3
α-helix	315-319	5
β-strand	325-326	2	2
α-helix	327	1
α-helix	330	1
β-strand	331	1	4
α-helix	332	1
β-strand	337	1	5
β-strand	338	1	4
β-strand	341-342	2	3
α-helix	348-350	3
α-helix	352	1
β-strand	353	1	5
α-helix	354-363	10
α-helix	373-401	29

Chain B: 25 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	12-21	10
α-helix	25-33	9
β-strand	39	1	1
α-helix	40-43	4
β-strand	45-50	6	6
β-strand	56-60	5	6
α-helix	65-75	11
β-strand	79-86	8	6
α-helix	90-92	3
β-strand	103-105	3	6
β-strand	108-113	6	7
α-helix	114-117	4
α-helix	131-146	16
α-helix	147-152	6
β-strand	157-161	5	7
β-strand	166-171	6	7
α-helix	174-177	4
α-helix	181-191	11
α-helix	211-224	14
α-helix	225-232	8
α-helix	238-244	7
α-helix	246-248	3
α-helix	252-264	13
α-helix	270-285	16
α-helix	290-309	20
β-strand	313	1	7
α-helix	315-319	5
β-strand	325-326	2	6
α-helix	327	1
α-helix	330	1
β-strand	331	1	8
α-helix	332	1
β-strand	337	1	9
β-strand	338	1	8
β-strand	341-342	2	7
α-helix	348-350	3
α-helix	352	1
β-strand	353	1	9
α-helix	354-363	10
α-helix	373-401	29

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
DNA primase small subunit	A, B	protein	414	Saccharomyces cerevisiae	P10363 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>4MM2_1 DNA primase small subunit (chains A, B)
GAMGSMTNSVKTNGPSSSDMEYYYKSLYPFKHIFNWLNHSPKPSRDMINREFAMAFRSGA
YKRYNSFNSVQDFKAQIEKANPDRFEIGAIYNKPPRERDTLLKSELKALEKELVFDIDMD
DYDAFRTCCSGAQVCSKCWKFISLAMKITNTALREDFGYKDFIWVFSGRRGAHCWVSDKR
ARALTDVQRRNVLDYVNVIRDRNTDKRLALKRPYHPHLARSLEQLKPFFVSIMLEEQNPW
EDDQHAIQTLLPALYDKQLIDSLKKYWLDNPRRSSKEKWNDIDQIATSLFKGPKQDSHII
KLRECKEDLVLMTLYPKLDVEVTKQTIHLLKAPFCIHPATGNVCVPIDESFAPEKAPKLI
DLQTEMEKNNDVSLTALQPFINQFQAYVSSLLKNELGSVKREREDDDEPASLDF

Ligands and cofactors

ID	Name	Formula	Copies
CD	Cadmium ion	Cd	10
CIT	Citric acid	C6 H8 O7	2

Primary citation

Crystal structure of yeast primase catalytic subunit. Park, K.R., An, J.Y., Lee, Y. et al. To be published.

Other PDB entries of the same protein (UniProt P10363 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4LIM 1.63 Å, Crystal structure of the catalytic subunit of yeast primase
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
8FOH 4.6 Å, Cryo-EM structure of S. cerevisiae DNA polymerase alpha-primase complex in the RNA…
8FOJ 4.8 Å, Cryo-EM structure of S. cerevisiae DNA polymerase alpha-primase complex in the post RNA…
8FOE 5.6 Å, Cryo-EM structure of S. cerevisiae DNA polymerase alpha-primase complex bound to a…

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