SMTL ID : 6skl.1

Cryo-EM structure of the CMG Fork Protection Complex at a replication fork - Conformation 1

Coordinates

PDB Format Compare

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: 7 residues within 4Å: Chain A: C.341, K.343, C.344, G.345, C.364, N.366, C.367 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.341, A:C.344, A:C.364, A:C.367 ZN.6: 6 residues within 4Å: Chain C: C.349, V.351, C.352, H.354, C.371, C.376 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.349, C:C.352, C:C.371, C:C.376 ZN.9: 7 residues within 4Å: Chain D: C.183, N.185, C.186, R.187, H.188, C.211, C.236 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.183, D:C.186, D:C.211, D:C.236 ZN.10: 7 residues within 4Å: Chain E: C.311, M.313, C.314, C.333, N.335, C.338, N.340 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:C.311, E:C.314, E:C.333, E:C.338 ZN.11: 6 residues within 4Å: Chain F: C.262, C.265, C.284, S.286, C.289, G.296 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:C.262, F:C.265, F:C.284, F:C.289

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

ANP.2: 24 residues within 4Å: Chain A: S.504, I.505, Y.506, H.508, P.545, G.546, T.547, A.548, K.549, S.550, Q.551, N.651, L.695, F.698, V.699 Chain E: L.565, E.657, Q.658, P.704, R.708, V.797, R.798, E.801 Ligands: MG.3 20 PLIP interactions: 12 interactions with chain A, 8 interactions with chain E Hydrogen bonds: A:Y.506, A:Y.506, A:G.546, A:T.547, A:T.547, A:A.548, A:K.549, A:K.549, A:S.550, A:Q.551, A:Q.551, A:N.651, E:Q.658, E:R.708, E:R.708, E:R.798, E:R.798, E:E.801, E:E.801 Salt bridges: E:R.798 ANP.4: 24 residues within 4Å: Chain B: S.370, I.371, Y.372, H.374, P.411, S.412, T.413, A.414, K.415, S.416, Q.417, N.517, I.561, H.564, V.565 Chain D: M.404, E.498, Q.499, T.545, R.549, I.650, R.651, E.654 Ligands: MG.5 20 PLIP interactions: 11 interactions with chain B, 9 interactions with chain D Hydrogen bonds: B:Y.372, B:Y.372, B:S.412, B:T.413, B:T.413, B:A.414, B:K.415, B:K.415, B:S.416, B:Q.417, B:N.517, D:Q.499, D:Q.499, D:R.549, D:R.549, D:R.651, D:R.651, D:E.654, D:E.654 Salt bridges: D:R.651 ANP.7: 27 residues within 4Å: Chain A: H.531, I.533, E.625, Q.626, P.672, R.676, V.807, R.808, E.811 Chain D: S.377, I.378, F.379, N.381, D.417, P.418, G.419, T.420, A.421, K.422, S.423, Q.424, N.524, I.568, H.571, V.572, I.575 Ligands: MG.8 21 PLIP interactions: 9 interactions with chain A, 12 interactions with chain D Hydrogen bonds: A:E.625, A:Q.626, A:Q.626, A:R.676, A:R.676, A:R.808, A:R.808, A:E.811, D:F.379, D:F.379, D:G.419, D:T.420, D:T.420, D:A.421, D:K.422, D:K.422, D:S.423, D:Q.424, D:Q.424, D:N.524 Salt bridges: A:R.808

3 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 6 residues within 4Å: Chain A: K.549, S.550 Chain E: Q.658, R.708, R.798 Ligands: ANP.2 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:S.550 MG.5: 6 residues within 4Å: Chain B: K.415, S.416 Chain D: Q.499, R.549, R.651 Ligands: ANP.4 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:S.416 MG.8: 4 residues within 4Å: Chain A: Q.626, R.676 Chain D: S.423 Ligands: ANP.7 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:S.423

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Baretic, D. et al., Cryo-EM Structure of the Fork Protection Complex Bound to CMG at a Replication Fork. Mol.Cell (2020)

Release Date

2020-05-06

Peptides

DNA replication licensing factor MCM2: A
DNA replication licensing factor MCM3: B
DNA replication licensing factor MCM4: C
Minichromosome maintenance protein 5: D
DNA replication licensing factor MCM6: E
DNA replication licensing factor MCM7: F
DNA replication complex GINS protein PSF1: G
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: K
DNA polymerase alpha-binding protein: LMN
Topoisomerase 1-associated factor 1: Q
Chromosome segregation in meiosis protein 3: 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
X

R
Y

DNA replication licensing factor MCM2

DNA replication licensing factor MCM3

DNA replication licensing factor MCM4

Minichromosome maintenance protein 5

DNA replication licensing factor MCM6

DNA replication licensing factor MCM7

DNA replication complex GINS protein PSF1

DNA replication complex GINS protein PSF2

DNA replication complex GINS protein PSF3

DNA replication complex GINS protein SLD5

Cell division control protein 45

DNA polymerase alpha-binding protein

Topoisomerase 1-associated factor 1

Chromosome segregation in meiosis protein 3

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