SMTL ID : 8ouw.1

Cryo-EM structure of CMG helicase bound to TIM-1/TIPN-1 and homodimeric DNSN-1 on fork DNA (Caenorhabditis elegans)

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

5 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.305, C.308, C.328, C.331 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.305, A:C.308, A:C.328, A:C.331 ZN.6: 4 residues within 4Å: Chain C: C.269, C.272, C.291, C.294 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.269, C:C.272, C:C.291, C:C.294 ZN.7: 4 residues within 4Å: Chain D: C.172, C.175, C.197, C.208 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.172, D:C.175, D:C.197, D:C.208 ZN.8: 4 residues within 4Å: Chain E: C.157, C.160, C.179, C.184 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:C.157, E:C.160, E:C.179, E:C.184 ZN.13: 5 residues within 4Å: Chain F: C.197, T.199, C.200, C.219, C.224 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:C.197, F:C.200, F:C.219, F:C.224

4 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 2 residues within 4Å: Chain B: S.355 Ligands: ANP.3 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:S.355 MG.4: 2 residues within 4Å: Chain C: S.476 Ligands: ANP.5 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:S.476 MG.9: 2 residues within 4Å: Chain E: S.404 Ligands: ANP.10 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:S.404 MG.12: 3 residues within 4Å: Chain F: S.397, D.454 Ligands: ANP.11 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:S.397

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

ANP.3: 17 residues within 4Å: Chain B: C.311, P.350, S.351, V.352, A.353, K.354, S.355, Q.356, N.456, V.504 Chain D: R.370, E.462, R.512, V.634, R.635, E.638 Ligands: MG.2 18 PLIP interactions: 12 interactions with chain B, 6 interactions with chain D Hydrogen bonds: B:C.311, B:C.311, B:S.351, B:V.352, B:A.353, B:K.354, B:K.354, B:K.354, B:S.355, B:Q.356, B:Q.356, B:N.456, D:R.370, D:R.512, D:R.512, D:R.635, D:R.635 Salt bridges: D:R.635 ANP.5: 20 residues within 4Å: Chain C: S.428, I.429, Y.430, P.471, G.472, T.473, S.474, K.475, S.476, Q.477, N.577, L.621, L.625 Chain F: M.378, E.472, R.523, P.613, R.614, L.617 Ligands: MG.4 21 PLIP interactions: 14 interactions with chain C, 7 interactions with chain F Hydrogen bonds: C:Y.430, C:Y.430, C:G.472, C:T.473, C:T.473, C:S.474, C:K.475, C:K.475, C:K.475, C:S.476, C:S.476, C:Q.477, C:Q.477, C:N.577, F:E.472, F:E.472, F:R.523, F:R.523, F:R.614, F:R.614 Salt bridges: F:R.614 ANP.10: 18 residues within 4Å: Chain C: E.551, R.602, R.692, E.695 Chain E: N.357, I.358, Y.359, D.398, P.399, S.400, T.401, A.402, K.403, S.404, Q.405, N.505, I.553 Ligands: MG.9 20 PLIP interactions: 7 interactions with chain C, 13 interactions with chain E Hydrogen bonds: C:E.551, C:R.602, C:R.602, C:R.692, C:R.692, C:E.695, E:Y.359, E:Y.359, E:N.361, E:S.400, E:T.401, E:T.401, E:A.402, E:K.403, E:K.403, E:S.404, E:S.404, E:Q.405, E:N.505 Salt bridges: C:R.692 ANP.11: 20 residues within 4Å: Chain B: E.430, Q.431, R.481, A.612, R.613, E.616 Chain F: E.352, I.353, F.354, P.392, G.393, V.394, A.395, K.396, S.397, Q.398, N.498, L.542, I.546 Ligands: MG.12 18 PLIP interactions: 13 interactions with chain F, 5 interactions with chain B Hydrogen bonds: F:F.354, F:F.354, F:G.393, F:V.394, F:A.395, F:K.396, F:K.396, F:K.396, F:K.396, F:S.397, F:S.397, F:Q.398, F:N.498, B:E.430, B:R.481, B:R.481, B:R.613 Salt bridges: B:R.613

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Xia, Y. et al., DNSN-1 recruits GINS for CMG helicase assembly during DNA replication initiation in Caenorhabditis elegans. Science (2023)

Release Date

2023-08-16

Peptides

DNA replication licensing factor MCM2: A
DNA replication licensing factor MCM3: B
DNA replication licensing factor mcm-4: C
DNA replication licensing factor mcm-5: D
DNA replication licensing factor mcm-6: E
DNA replication licensing factor MCM7: F
Probable DNA replication complex GINS protein PSF1: G
Probable DNA replication complex GINS protein PSF2: H
DNA replication complex GINS protein PSF3: I
DNA replication complex GINS protein SLD5: J
Cell division control protein 45 homolog: K
Downstream Neighbor of SoN homolog: LMN
Protein timeless homolog: Q
Protein TIPIN homolog: R

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
2

B
3

C
4

D
5

E
6

F
7

G
A

H
B

I
C

J
D

K
E

L
F

M
G

N
H

Q
K

R
L

DNA replication licensing factor MCM2

DNA replication licensing factor MCM3

DNA replication licensing factor mcm-4

DNA replication licensing factor mcm-5

DNA replication licensing factor mcm-6

DNA replication licensing factor MCM7

Probable DNA replication complex GINS protein PSF1

Probable DNA replication complex GINS protein PSF2

DNA replication complex GINS protein PSF3

DNA replication complex GINS protein SLD5

Cell division control protein 45 homolog

Downstream Neighbor of SoN homolog

Protein timeless homolog

Protein TIPIN homolog