SMTL ID : 7rip.1

RNA polymerase II elongation complex with hairpin polyamide Py-Im 1, scaffold 1 soaked with CTP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.30 Å

Oligo State

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

Ligands

1 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 5 residues within 4Å: Chain A: G.9, C.10 Chain D: D.481, D.483, D.485 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:D.483, D:D.483

1 x 5N0: 3-({3-[(3-{[4-({4-[(4-{[4-({(2R)-2-amino-4-[(1-methyl-4-{[1-methyl-4-({1-methyl-4-[(1-methyl-1H-imidazole-2-carbonyl)amino]-1H-imidazole-2-carbonyl}amino)-1H-pyrrole-2-carbonyl]amino}-1H-pyrrole-2-carbonyl)amino]butanoyl}amino)-1-methyl-1H-imidazole-2-carbonyl]amino}-1-methyl-1H-pyrrole-2-carbonyl)amino]-1-methyl-1H-pyrrole-2-carbonyl}amino)-1-methyl-1H-pyrrole-2-carbonyl]amino}propyl)(methyl)amino]propyl}carbamoyl)benzoic acid(Non-covalent)

5N0.2: 19 residues within 4Å: Chain B: T.11, G.12, G.13, T.14, C.15, A.16, T.17 Chain C: G.6, A.7, C.8, C.9, A.10, G.11, A.12, G.13, A.14 Chain D: R.1386, H.1387, R.1391 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:R.1386

8 x ZN: ZINC ION(Non-covalent)

ZN.3: 5 residues within 4Å: Chain D: C.107, H.109, C.110, C.148, C.167 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:C.107, D:C.110, D:C.167 ZN.4: 4 residues within 4Å: Chain D: C.67, C.70, C.77, H.80 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.67, D:C.70, D:C.77, D:H.80 ZN.6: 4 residues within 4Å: Chain E: C.1163, C.1166, C.1182, C.1185 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:C.1163, E:C.1166, E:C.1182, E:C.1185 ZN.7: 5 residues within 4Å: Chain F: C.86, C.88, H.91, C.92, C.95 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:C.86, F:C.88, F:C.92, F:C.95 ZN.8: 5 residues within 4Å: Chain J: C.7, C.10, C.29, T.31, C.32 4 PLIP interactions: 4 interactions with chain J Metal complexes: J:C.7, J:C.10, J:C.29, J:C.32 ZN.9: 5 residues within 4Å: Chain J: C.75, C.78, S.80, C.103, C.106 4 PLIP interactions: 4 interactions with chain J Metal complexes: J:C.75, J:C.78, J:C.103, J:C.106 ZN.10: 5 residues within 4Å: Chain K: C.7, C.10, R.43, C.45, C.46 4 PLIP interactions: 4 interactions with chain K Metal complexes: K:C.7, K:C.10, K:C.45, K:C.46 ZN.11: 5 residues within 4Å: Chain M: C.31, C.34, S.36, C.48, C.51 4 PLIP interactions: 4 interactions with chain M Metal complexes: M:C.31, M:C.34, M:C.48, M:C.51

1 x PPV: PYROPHOSPHATE(Non-covalent)

PPV.5: 4 residues within 4Å: Chain D: D.481, K.752 Chain E: S.1019, R.1020 7 PLIP interactions: 4 interactions with chain E, 3 interactions with chain D Hydrogen bonds: E:S.1019, E:S.1019, D:D.481 Salt bridges: E:R.1020, E:R.1020, D:K.752, D:K.752

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Oh, J. et al., RNA polymerase II trapped on a molecular treadmill: Structural basis of persistent transcriptional arrest by a minor groove DNA binder. Proc.Natl.Acad.Sci.USA (2022)

Release Date

2022-01-12

Peptides

DNA-directed RNA polymerase II subunit RPB1: D
DNA-directed RNA polymerase II subunit RPB2: E
DNA-directed RNA polymerase II subunit RPB3: F
DNA-directed RNA polymerases I, II, and III subunit RPABC1: G
DNA-directed RNA polymerases I, II, and III subunit RPABC2: H
DNA-directed RNA polymerases I, II, and III subunit RPABC3: I
DNA-directed RNA polymerase II subunit RPB9: J
DNA-directed RNA polymerases I, II, and III subunit RPABC5: K
DNA-directed RNA polymerase II subunit RPB11: L
DNA-directed RNA polymerases I, II, and III subunit RPABC4: M

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

D
A

E
B

F
C

G
E

H
F

I
H

J
I

K
J

L
K

M
L

DNA-directed RNA polymerase II subunit RPB1

DNA-directed RNA polymerase II subunit RPB2

DNA-directed RNA polymerase II subunit RPB3

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

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

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

DNA-directed RNA polymerase II subunit RPB9

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

DNA-directed RNA polymerase II subunit RPB11

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

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