SMTL ID : 8xgc.1

Structure of yeast replisome associated with FACT and histone hexamer, Composite map

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-1-1-1-1-1-1-1-1-1-1-3-1-1-1-1-1-2-2-1-1-mer

Ligands

7 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.341, C.344, C.364, C.367 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:C.341, A:C.344, A:C.364 ZN.4: 4 residues within 4Å: Chain C: C.349, C.352, 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.5: 4 residues within 4Å: Chain D: C.183, C.186, 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.7: 4 residues within 4Å: Chain E: C.311, C.314, C.333, C.338 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:C.311, E:C.314, E:C.333, E:C.338 ZN.9: 4 residues within 4Å: Chain F: C.262, C.265, C.284, C.289 3 PLIP interactions: 3 interactions with chain F Metal complexes: F:C.262, F:C.265, F:C.289 ZN.11: 4 residues within 4Å: Chain G: C.2108, C.2111, C.2130, C.2133 3 PLIP interactions: 3 interactions with chain G Metal complexes: G:C.2108, G:C.2111, G:C.2130 ZN.12: 4 residues within 4Å: Chain G: C.2164, C.2167, C.2179, C.2181 1 PLIP interactions: 1 interactions with chain G Metal complexes: G:C.2164

5 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.2: 17 residues within 4Å: Chain A: S.504, I.505, Y.506, P.545, G.546, T.547, A.548, K.549, S.550, Q.551, V.699 Chain E: L.565, E.657, Q.658, V.797, R.798, E.801 16 PLIP interactions: 11 interactions with chain A, 5 interactions with chain E Hydrogen bonds: A:Y.506, A:Y.506, A:G.546, A:A.548, A:K.549, A:S.550, A:S.550, A:S.550, A:Q.551, A:E.608, E:E.657, E:Q.658, E:E.801 Salt bridges: A:K.549, E:R.798, E:R.798 ADP.3: 19 residues within 4Å: Chain B: S.370, Y.372, P.411, S.412, A.414, K.415, S.416, Q.417, D.473, A.515, I.561, H.564, V.565 Chain D: E.498, Q.499, R.549, I.650, R.651, E.654 17 PLIP interactions: 11 interactions with chain B, 6 interactions with chain D Hydrogen bonds: B:S.370, B:Y.372, B:S.412, B:A.414, B:K.415, B:S.416, B:S.416, B:D.473, B:N.517, D:E.498, D:Q.499, D:E.654 Salt bridges: B:K.415, B:K.415, D:R.549, D:R.549, D:R.651 ADP.6: 17 residues within 4Å: Chain A: H.531, E.625, R.676, V.807, R.808, E.811 Chain D: S.377, I.378, F.379, P.418, G.419, T.420, A.421, K.422, S.423, Q.424, V.572 14 PLIP interactions: 10 interactions with chain D, 4 interactions with chain A Hydrogen bonds: D:F.379, D:F.379, D:G.419, D:T.420, D:A.421, D:K.422, D:S.423, D:Q.424, D:Q.424, A:H.531, A:E.625 Salt bridges: D:K.422, A:R.676, A:R.808 ADP.8: 16 residues within 4Å: Chain C: R.701, T.795, R.796 Chain E: A.536, V.537, F.538, D.576, P.577, S.578, T.579, S.580, K.581, S.582, Q.583, L.727, I.731 10 PLIP interactions: 8 interactions with chain E, 2 interactions with chain C Hydrogen bonds: E:F.538, E:F.538, E:T.579, E:S.580, E:K.581, E:S.582, E:Q.583, E:Q.583 Salt bridges: C:R.701, C:R.796 ADP.10: 15 residues within 4Å: Chain B: R.542, A.699, R.700, E.703 Chain F: E.421, I.422, P.462, G.463, V.464, A.465, K.466, S.467, Q.468, L.612, V.616 13 PLIP interactions: 6 interactions with chain B, 7 interactions with chain F Hydrogen bonds: B:R.700, B:E.703, B:E.703, F:E.421, F:G.463, F:V.464, F:A.465, F:K.466, F:S.467, F:Q.468 Salt bridges: B:R.542, B:R.542, B:R.700

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Li, N. et al., Parental histone transfer caught at the replication fork. Nature (2024)

Release Date

2024-02-14

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 polymerase epsilon catalytic subunit A: G
DNA polymerase epsilon subunit B: 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
Cell division control protein 45: M
DNA polymerase alpha-binding protein: NOP
Topoisomerase 1-associated factor 1: Q
Chromosome segregation in meiosis protein 3: R
Mediator of replication checkpoint protein 1: S
FACT complex subunit SPT16: T
FACT complex subunit POB3: U
Histone H3: VZ
Histone H4: W0
Histone H2A.1: X
Histone H2B.2: Y

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
2

B
3

C
4

D
5

E
6

F
7

G
8

H
9

I
A

J
B

K
C

L
D

M
E

N
F

O
G

P
H

Q
I

R
J

S
K

T
L

U
M

V
N

Z
R

W
O

0
S

X
P

Y
Q

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 polymerase epsilon catalytic subunit A

DNA polymerase epsilon subunit B

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

Mediator of replication checkpoint protein 1

FACT complex subunit SPT16

FACT complex subunit POB3

Histone H3

Histone H4

Histone H2A.1

Histone H2B.2

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