SMTL ID : 7rim.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.90 Å

Oligo State

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

Ligands

1 x A- U- C- G- A- G- A- G- G: RNA(Non-covalent)

A-U-C-G-A-G-A-G-G.1: 24 residues within 4Å: Chain A: G.20, C.21, C.22, T.23, C.24, T.25, C.26, G.27, A.28, T.29 Chain C: R.446, Q.447, D.483, D.485 Chain D: G.478, Q.481, R.504, Q.776, K.979, K.987, H.1097, Q.1112, R.1124 Ligands: MG.5 Protein-ligand interaction information (PLIP) not available

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: 22 residues within 4Å: Chain A: T.9, C.10, T.11, G.12, G.13, T.14, C.15, A.16, T.17 Chain B: T.5, G.6, A.7, C.8, C.9, A.10, G.11, A.12, G.13, A.14 Chain C: R.1386, H.1387, E.1404 No protein-ligand interaction detected (PLIP)

8 x ZN: ZINC ION(Non-covalent)

ZN.3: 5 residues within 4Å: Chain C: C.107, H.109, C.110, C.148, C.167 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:C.107, C:C.110, C:C.167 ZN.4: 4 residues within 4Å: Chain C: C.67, C.70, C.77, H.80 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.67, C:C.70, C:C.77, C:H.80 ZN.6: 5 residues within 4Å: Chain D: C.1163, I.1165, C.1166, C.1182, C.1185 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.1163, D:C.1166, D:C.1182, D:C.1185 ZN.7: 5 residues within 4Å: Chain E: C.86, C.88, H.91, C.92, C.95 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:C.86, E:C.88, E:C.92, E:C.95 ZN.8: 5 residues within 4Å: Chain I: C.7, C.10, C.29, T.31, C.32 4 PLIP interactions: 4 interactions with chain I Metal complexes: I:C.7, I:C.10, I:C.29, I:C.32 ZN.9: 5 residues within 4Å: Chain I: C.75, C.78, S.80, C.103, C.106 4 PLIP interactions: 4 interactions with chain I Metal complexes: I:C.75, I:C.78, I:C.103, I:C.106 ZN.10: 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.11: 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

1 x MG: MAGNESIUM ION(Non-covalent)

MG.5: 4 residues within 4Å: Chain C: D.481, D.483, D.485 Ligands: A-U-C-G-A-G-A-G-G.1 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:D.483, C:D.483, C:D.485

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

C
A

D
B

E
C

F
E

G
F

H
H

I
I

J
J

K
K

L
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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