SMTL ID : 8b9d.1

Human replisome bound by Pol Alpha

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-3-1-mer

Ligands

3 x ANP: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER(Non-covalent)

ANP.1: 22 residues within 4Å: Chain A: S.484, I.485, Y.486, D.524, P.525, G.526, T.527, A.528, K.529, S.530, Q.531, N.631, L.675, V.679 Chain E: L.386, E.478, Q.479, R.529, V.618, R.619, E.622 Ligands: MG.2 19 PLIP interactions: 13 interactions with chain A, 6 interactions with chain E Hydrogen bonds: A:Y.486, A:Y.486, A:D.524, A:G.526, A:T.527, A:T.527, A:A.528, A:K.529, A:K.529, A:S.530, A:Q.531, A:Q.531, A:N.631, E:Q.479, E:R.529, E:R.529, E:R.619, E:R.619, E:E.622 ANP.3: 23 residues within 4Å: Chain B: S.306, I.307, H.308, D.346, P.347, S.348, V.349, A.350, K.351, S.352, Q.353, N.453, I.497, H.500, V.501 Chain D: R.371, E.463, Q.464, R.513, V.610, R.611, E.614 Ligands: MG.4 21 PLIP interactions: 12 interactions with chain B, 9 interactions with chain D Hydrogen bonds: B:H.308, B:H.308, B:D.346, B:S.348, B:V.349, B:A.350, B:K.351, B:K.351, B:S.352, B:S.352, B:Q.353, B:N.453, D:R.371, D:R.371, D:R.513, D:R.513, D:R.611, D:R.611, D:E.614, D:E.614 Salt bridges: D:R.611 ANP.7: 24 residues within 4Å: Chain A: H.511, V.513, E.605, Q.606, P.652, R.656, V.764, R.765, E.768 Chain D: S.342, I.343, F.344, P.383, G.384, T.385, A.386, K.387, S.388, Q.389, N.489, L.532, V.536, L.539 Ligands: MG.8 22 PLIP interactions: 13 interactions with chain D, 9 interactions with chain A Hydrogen bonds: D:F.344, D:F.344, D:D.382, D:G.384, D:T.385, D:T.385, D:A.386, D:K.387, D:K.387, D:S.388, D:S.388, D:Q.389, D:Q.389, A:H.511, A:Q.606, A:R.656, A:R.656, A:R.765, A:R.765, A:E.768, A:E.768 Salt bridges: A:R.765

3 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 2 residues within 4Å: Chain A: S.530 Ligands: ANP.1 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:S.530 MG.4: 4 residues within 4Å: Chain B: S.352 Chain D: R.513, R.611 Ligands: ANP.3 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:S.352 MG.8: 4 residues within 4Å: Chain A: Q.606, R.656 Chain D: S.388 Ligands: ANP.7 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:S.388

4 x ZN: ZINC ION(Non-covalent)

ZN.5: 7 residues within 4Å: Chain C: C.306, V.308, C.309, H.311, C.328, R.330, C.331 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.306, C:C.309, C:C.328, C:C.331 ZN.6: 5 residues within 4Å: Chain D: C.172, S.174, C.175, C.197, C.207 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:C.175, D:C.197, D:C.207 ZN.9: 6 residues within 4Å: Chain E: C.158, C.161, C.180, N.182, C.185, N.187 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:C.158, E:C.161, E:C.180, E:C.185 ZN.10: 5 residues within 4Å: Chain F: C.184, C.187, C.206, S.208, C.211 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:C.184, F:C.187, F:C.206, F:C.211

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jones, M.L. et al., How Pol alpha-primase is targeted to replisomes to prime eukaryotic DNA replication. Mol.Cell (2023)

Release Date

2023-08-09

Peptides

DNA replication licensing factor MCM2: A
DNA replication licensing factor MCM3: B
DNA replication licensing factor MCM4: C
DNA replication licensing factor MCM5: D
DNA replication licensing factor MCM6: E
DNA replication licensing factor MCM7: F
DNA polymerase alpha subunit B: G
Cell division control protein 45 homolog: H
DNA replication complex GINS protein PSF1: I
DNA replication complex GINS protein PSF2: J
DNA replication complex GINS protein PSF3: K
DNA replication complex GINS protein SLD5: L
Protein timeless homolog: M
TIMELESS-interacting protein: N
DNA primase large subunit: Q
Claspin: R
DNA primase small subunit: S
WD repeat and HMG-box DNA-binding protein 1: TVW
DNA polymerase alpha catalytic subunit: U

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
2

B
3

C
4

D
5

E
6

F
7

G
A

H
C

I
D

J
E

K
F

L
G

M
K

N
L

Q
P

R
Q

S
O

T
H

V
J

W
I

U
B

DNA replication licensing factor MCM2

DNA replication licensing factor MCM3

DNA replication licensing factor MCM4

DNA replication licensing factor MCM5

DNA replication licensing factor MCM6

DNA replication licensing factor MCM7

DNA polymerase alpha subunit B

Cell division control protein 45 homolog

DNA replication complex GINS protein PSF1

DNA replication complex GINS protein PSF2

DNA replication complex GINS protein PSF3

DNA replication complex GINS protein SLD5

Protein timeless homolog

TIMELESS-interacting protein

DNA primase large subunit

Claspin

DNA primase small subunit

WD repeat and HMG-box DNA-binding protein 1

DNA polymerase alpha catalytic subunit

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