SMTL ID : 3po3.1

Arrested RNA Polymerase II reactivation intermediate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.30 Å

Oligo State

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

Ligands

1 x C- C- C- C- C: RNA product strand(Non-covalent)

C-C-C-C-C.1: 20 residues within 4Å: Chain A: R.446, P.448, N.479, D.483, D.485, T.831 Chain B: Y.486, Q.776, K.979, K.987, R.1096, H.1097 Chain N: R.156, S.157 Chain O: G.14, G.15, T.16, G.17, U.18 Ligands: MG.4 Protein-ligand interaction information (PLIP) not available

9 x ZN: ZINC ION(Non-covalent)

ZN.2: 4 residues within 4Å: Chain A: C.107, C.110, C.148, C.167 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.107, A:C.110, A:C.148, A:C.167 ZN.3: 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.7: 4 residues within 4Å: Chain B: C.1163, C.1166, C.1182, C.1185 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.1163, B:C.1166, B:C.1182, B:C.1185 ZN.9: 5 residues within 4Å: Chain C: C.86, C.88, H.91, C.92, C.95 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.86, C:C.88, C:C.92, C:C.95 ZN.10: 5 residues within 4Å: Chain I: C.7, R.8, C.10, C.29, 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.11: 4 residues within 4Å: Chain I: C.75, C.78, 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.12: 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.13: 5 residues within 4Å: Chain L: C.31, C.34, S.36, 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 ZN.15: 4 residues within 4Å: Chain N: C.140, C.143, C.168, C.171 4 PLIP interactions: 4 interactions with chain N Metal complexes: N:C.140, N:C.143, N:C.168, N:C.171

1 x MG: MAGNESIUM ION(Non-covalent)

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

2 x ACT: ACETATE ION(Non-functional Binders)

ACT.5: 5 residues within 4Å: Chain A: Q.935, K.938, D.939, F.942 Chain E: R.207 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain E Hydrophobic interactions: A:F.942 Hydrogen bonds: A:Q.935 Salt bridges: A:K.938, A:R.1023, E:R.207 ACT.8: 5 residues within 4Å: Chain A: E.16 Chain B: Y.1217, D.1219, S.1221 Chain D: R.14 4 PLIP interactions: 1 interactions with chain D, 3 interactions with chain B Salt bridges: D:R.14 Hydrophobic interactions: B:Y.1217 Hydrogen bonds: B:D.1219, B:S.1221

1 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)

EPE.6: 9 residues within 4Å: Chain A: R.28, A.29, S.31, V.32, A.33, K.34, R.36, R.57 Chain B: K.1183 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:A.29, A:K.34 Salt bridges: A:R.36, A:R.57

1 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.14: 4 residues within 4Å: Chain L: K.28, S.39, L.40, S.41 1 PLIP interactions: 1 interactions with chain L Hydrogen bonds: L:S.39

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cheung, A.C. et al., Structural basis of RNA polymerase II backtracking, arrest and reactivation. Nature (2011)

Release Date

2011-03-02

Peptides

DNA-directed RNA polymerase II subunit RPB1: A
DNA-directed RNA polymerase II subunit RPB2: B
DNA-directed RNA polymerase II subunit RPB3: C
DNA-directed RNA polymerase II subunit RPB4: 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 II subunit RPB7: 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
Transcription elongation factor S-II: N

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

N
S

DNA-directed RNA polymerase II subunit RPB1

DNA-directed RNA polymerase II subunit RPB2

DNA-directed RNA polymerase II subunit RPB3

DNA-directed RNA polymerase II subunit RPB4

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

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

DNA-directed RNA polymerase II subunit RPB7

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

Transcription elongation factor S-II

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