SMTL ID : 7z2z.1

Structure of yeast RNA Polymerase III-DNA-Ty1 integrase complex (Pol III-DNA-IN1) at 3.1 A

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

7 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.67, C.70, C.77, H.80 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.67, A:C.70, A:C.77, A:H.80 ZN.2: 4 residues within 4Å: Chain A: C.107, C.110, C.154, C.157 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.107, A:C.110, A:C.154, A:C.157 ZN.5: 4 residues within 4Å: Chain B: C.1095, C.1098, C.1107, C.1110 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.1095, B:C.1098, B:C.1107, B:C.1110 ZN.7: 5 residues within 4Å: Chain I: C.5, C.8, C.26, S.28, C.29 5 PLIP interactions: 5 interactions with chain I Metal complexes: I:C.5, I:C.8, I:C.26, I:S.28, I:C.29 ZN.8: 4 residues within 4Å: Chain I: C.69, C.75, C.100, C.103 4 PLIP interactions: 4 interactions with chain I Metal complexes: I:C.69, I:C.75, I:C.100, I:C.103 ZN.9: 4 residues within 4Å: Chain J: C.7, C.10, C.45, C.46 4 PLIP interactions: 4 interactions with chain J Metal complexes: J:C.7, J:C.10, J:C.45, J:C.46 ZN.10: 4 residues within 4Å: Chain L: C.31, C.34, C.48, C.51 4 PLIP interactions: 4 interactions with chain L Metal complexes: L:C.31, L:C.34, L:C.48, L:C.51

2 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 5 residues within 4Å: Chain A: D.511, D.513, D.515 Chain R: A.10 Ligands: MG.6 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.511, A:D.511, A:D.513, A:D.513, A:D.515 MG.6: 6 residues within 4Å: Chain A: D.511, D.513 Chain I: D.91, E.92 Chain R: A.10 Ligands: MG.3 4 PLIP interactions: 2 interactions with chain I, 2 interactions with chain A Metal complexes: I:D.91, I:E.92, A:D.511, A:D.513

1 x 4QM: (3R,5S,7R,8R,9S,10S,12S,13R,14S,17R)-10,13-dimethyl-17-[(2R)-pentan-2-yl]-2,3,4,5,6,7,8,9,11,12,14,15,16,17-tetradecahydro-1H-cyclopenta[a]phenanthrene-3,7,12-triol(Non-covalent)

4QM.4: 5 residues within 4Å: Chain A: K.1134, D.1277, Y.1298, H.1318, S.1324 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:K.1134, A:Y.1298

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nguyen, P.Q. et al., Structural basis of Ty1 integrase tethering to RNA polymerase III for targeted retrotransposon integration. Nat Commun (2023)

Release Date

2023-04-05

Peptides

DNA-directed RNA polymerase III subunit RPC1: A
DNA-directed RNA polymerase III subunit RPC2: B
DNA-directed RNA polymerases I and III subunit RPAC1: C
DNA-directed RNA polymerase III subunit RPC9: D
DNA-directed RNA polymerases I, II, and III subunit RPABC1: E
DNA-directed RNA polymerases I, II, and III subunit RPABC2: F
DNA-directed RNA polymerase III subunit RPC8: G
DNA-directed RNA polymerases I, II, and III subunit RPABC3: H
DNA-directed RNA polymerase III subunit RPC10: I
DNA-directed RNA polymerases I, II, and III subunit RPABC5: J
DNA-directed RNA polymerases I and III subunit RPAC2: K
DNA-directed RNA polymerases I, II, and III subunit RPABC4: L
DNA-directed RNA polymerase III subunit RPC5: M
DNA-directed RNA polymerase III subunit RPC4: N
DNA-directed RNA polymerase III subunit RPC3: O
DNA-directed RNA polymerase III subunit RPC6: P
DNA-directed RNA polymerase III subunit RPC7: Q
Integrase: U
Unknown RNA polymerase III chain: V

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

I
I

J
J

K
K

L
L

M
M

N
N

O
O

P
P

Q
Q

U
W

V
X

DNA-directed RNA polymerase III subunit RPC1

DNA-directed RNA polymerase III subunit RPC2

DNA-directed RNA polymerases I and III subunit RPAC1

DNA-directed RNA polymerase III subunit RPC9

DNA-directed RNA polymerases I, II, and III subunit RPABC1

DNA-directed RNA polymerases I, II, and III subunit RPABC2

DNA-directed RNA polymerase III subunit RPC8

DNA-directed RNA polymerases I, II, and III subunit RPABC3

DNA-directed RNA polymerase III subunit RPC10

DNA-directed RNA polymerases I, II, and III subunit RPABC5

DNA-directed RNA polymerases I and III subunit RPAC2

DNA-directed RNA polymerases I, II, and III subunit RPABC4

DNA-directed RNA polymerase III subunit RPC5

DNA-directed RNA polymerase III subunit RPC4

DNA-directed RNA polymerase III subunit RPC3

DNA-directed RNA polymerase III subunit RPC6

DNA-directed RNA polymerase III subunit RPC7

Integrase

Unknown RNA polymerase III chain

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