SMTL ID : 5c3e.1

Crystal structure of a transcribing RNA Polymerase II complex reveals a complete transcription bubble

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.70 Å

Oligo State

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

Ligands

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

U-C-G-A-G-A-G-G-A.1: 25 residues within 4Å: Chain A: R.320, R.446, D.481, D.483, D.485 Chain B: A.477, Q.481, Q.531, Q.776, K.979, K.987, R.1096, H.1097, V.1113 Chain N: A.18, T.19, C.20, C.21, T.22, C.23, T.24, C.25, G.26, A.27 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: M.108, C.110, C.148, C.167 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:C.110, A:C.167 ZN.3: 4 residues within 4Å: Chain A: C.67, C.70, C.77, H.80 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:C.67, A:H.80 ZN.6: 5 residues within 4Å: Chain B: C.1163, C.1166, T.1170, C.1182, C.1185 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:C.1163, B:C.1182, B:C.1185 ZN.7: 2 residues within 4Å: Chain C: C.88, K.94 No protein-ligand interaction detected (PLIP) ZN.8: 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.9: 4 residues within 4Å: Chain I: C.7, C.10, C.29, C.32 3 PLIP interactions: 3 interactions with chain I Metal complexes: I:C.10, I:C.29, I:C.32 ZN.10: 5 residues within 4Å: Chain I: C.75, C.78, S.80, C.106, H.108 3 PLIP interactions: 3 interactions with chain I Metal complexes: I:C.75, I:C.78, I:C.106 ZN.11: 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.12: 7 residues within 4Å: Chain L: C.31, A.32, E.33, C.34, S.36, C.48, C.51 2 PLIP interactions: 2 interactions with chain L Metal complexes: L:C.34, L:C.51

2 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 3 residues within 4Å: Chain A: D.481, D.483 Ligands: U-C-G-A-G-A-G-G-A.1 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.481, A:D.481 MG.5: 3 residues within 4Å: Chain A: T.1394, G.1395, L.1418 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Barnes, C.O. et al., Crystal Structure of a Transcribing RNA Polymerase II Complex Reveals a Complete Transcription Bubble. Mol.Cell (2015)

Release Date

2015-08-26

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

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

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

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