SMTL ID : 8qj7.1

Cryo-EM structure of human DNA polymerase alpha-primase in pre-initiation stage 1

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-1-mer

Ligands

3 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: C.121, C.122, C.128, K.130, C.131 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.121, A:C.122, A:C.128, A:C.131 ZN.5: 7 residues within 4Å: Chain B: C.1283, T.1285, C.1286, T.1288, C.1310, N.1312, C.1315 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.1283, B:C.1286, B:C.1310, B:C.1315 ZN.6: 7 residues within 4Å: Chain B: C.1348, C.1353, N.1355, C.1371, A.1373, C.1374, A.1377 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.1348, B:C.1353, B:C.1371, B:C.1374

2 x MN: MANGANESE (II) ION(Non-covalent)

MN.2: 5 residues within 4Å: Chain A: D.109, D.111, S.160, H.166 Ligands: ATP.4 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.109, A:H.166 MN.3: 3 residues within 4Å: Chain A: D.111, D.306 Ligands: ATP.4 No protein-ligand interaction detected (PLIP)

1 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.4: 19 residues within 4Å: Chain A: K.77, D.109, I.110, D.111, S.160, G.161, R.162, R.163, G.164, V.165, H.166, D.306, V.309, H.315, L.317, K.318, H.324 Ligands: MN.2, MN.3 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:D.111, A:S.160, A:S.160, A:R.162, A:R.162, A:R.163, A:G.164, A:H.166 Salt bridges: A:R.162, A:R.163, A:R.163, A:H.166, A:H.324

1 x SF4: IRON/SULFUR CLUSTER(Non-covalent)

SF4.7: 12 residues within 4Å: Chain D: P.285, P.286, C.287, C.367, I.370, I.371, C.384, P.385, Q.421, C.424, L.441, P.444 4 PLIP interactions: 4 interactions with chain D, Metal complexes: D:C.287, D:C.367, D:C.384, D:C.424

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yin, Z. et al., CryoEM insights into RNA primer synthesis by the human primosome. Febs J. (2024)

Release Date

2024-02-21

Peptides

DNA primase small subunit: A
DNA polymerase alpha catalytic subunit: B
DNA polymerase alpha subunit B: C
DNA primase large subunit: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
A

C
B

D
D

DNA primase small subunit

DNA polymerase alpha catalytic subunit

DNA polymerase alpha subunit B

DNA primase large subunit

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