SMTL ID : 5c4j.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 4.00 Å

Oligo State

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

Ligands

1 x U- C- G- A- G- A- G- G- A: RNA (5'-R(P*UP*CP*GP*AP*GP*AP*GP*GP*A)-3')(Non-covalent)

U-C-G-A-G-A-G-G-A.1: 23 residues within 4Å: Chain A: F.252, K.323, D.483 Chain B: A.477, Q.481, P.528, Q.531, Q.776, K.979, R.1096, H.1097, R.1124 Chain L: A.19, T.20, C.21, C.22, T.23, C.24, T.25, C.26, G.27, A.28 Ligands: MG.11 Protein-ligand interaction information (PLIP) not available

9 x ZN: ZINC ION(Non-covalent)(Non-functional Binders)

ZN.2: 5 residues within 4Å: Chain A: C.107, M.108, C.110, C.148, C.167 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:C.107, A:C.110 ZN.3: 6 residues within 4Å: Chain A: C.67, Q.68, C.70, C.77, H.80 Chain B: A.1173 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:C.67 ZN.4: 5 residues within 4Å: Chain B: C.1163, C.1166, T.1170, C.1182, C.1185 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:C.1163 ZN.5: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) ZN.6: 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.7: 5 residues within 4Å: Chain G: C.7, D.9, C.10, C.29, C.32 4 PLIP interactions: 4 interactions with chain G Metal complexes: G:C.7, G:C.10, G:C.29, G:C.32 ZN.8: 5 residues within 4Å: Chain G: C.75, C.78, S.80, C.103, C.106 1 PLIP interactions: 1 interactions with chain G Metal complexes: G:C.106 ZN.9: 4 residues within 4Å: Chain H: C.7, C.10, C.45, C.46 3 PLIP interactions: 3 interactions with chain H Metal complexes: H:C.7, H:C.10, H:C.45 ZN.10: 4 residues within 4Å: Chain J: C.31, C.34, C.48, C.51 2 PLIP interactions: 2 interactions with chain J Metal complexes: J:C.34, J:C.48

1 x MG: MAGNESIUM ION(Non-covalent)

MG.11: 4 residues within 4Å: Chain A: D.481, D.483, D.485 Ligands: U-C-G-A-G-A-G-G-A.1 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 polymerases I, II, and III subunit RPABC1: D
DNA-directed RNA polymerases I, II, and III subunit RPABC2: E
DNA-directed RNA polymerases I, II, and III subunit RPABC3: F
DNA-directed RNA polymerase II subunit RPB9: G
DNA-directed RNA polymerases I, II, and III subunit RPABC5: H
DNA-directed RNA polymerase II subunit RPB11: I
DNA-directed RNA polymerases I, II, and III subunit RPABC4: J

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
E

E
F

F
H

G
I

H
J

I
K

J
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

Related Entries With Identical Sequence