SMTL ID : 9ja1.1

The RNA polymerase II elongation complex from Saccharomyces cerevisiae

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

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

A-U-C-G-A-G-A-G-G.1: 24 residues within 4Å: Chain A: I.250, F.252, R.320, R.446, Q.447, D.485 Chain B: R.476, A.477, Q.481, Q.776, K.979, K.987, H.1097 Chain L: C.42, C.43, T.44, C.45, T.46, C.47, G.48, A.49, T.50 Ligands: MG.9, ATP.10 Protein-ligand interaction information (PLIP) not available

6 x ZN: ZINC ION

ZN.2: 4 residues within 4Å: Chain A: C.107, C.110, C.148, C.167 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:C.107, A:C.110, 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.5: 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.6: 4 residues within 4Å: Chain C: C.86, C.88, C.92, C.95 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:C.86, C:C.88, C:C.95 ZN.7: 4 residues within 4Å: Chain G: C.7, C.10, C.45, C.46 4 PLIP interactions: 4 interactions with chain G Metal complexes: G:C.7, G:C.10, G:C.45, G:C.46 ZN.8: 5 residues within 4Å: Chain I: C.31, E.33, C.34, C.48, C.51 5 PLIP interactions: 5 interactions with chain I Metal complexes: I:C.31, I:E.33, I:C.34, I:C.48, I:C.51

2 x MG: MAGNESIUM ION

MG.4: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.9: 2 residues within 4Å: Chain B: G.530 Ligands: A-U-C-G-A-G-A-G-G.1 No protein-ligand interaction detected (PLIP)

1 x ATP: ADENOSINE-5'-TRIPHOSPHATE

ATP.10: 16 residues within 4Å: Chain A: R.446, P.448, N.479, D.481, D.483, T.827, L.1081, F.1084, H.1085 Chain B: R.766, Y.769, K.987, R.1020 Chain L: T.41, C.42 Ligands: A-U-C-G-A-G-A-G-G.1 10 PLIP interactions: 6 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:R.446, A:R.446, A:N.479, A:D.481, A:D.483 Salt bridges: A:H.1085, B:R.766, B:K.987, B:K.987, B:R.1020

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ma, J. et al., The RNA polymerase II elongation complex from Saccharomyces cerevisiae. To Be Published

Release Date

2024-09-04

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 polymerases I, II, and III subunit RPABC5: G
DNA-directed RNA polymerase II subunit RPB11: H
DNA-directed RNA polymerases I, II, and III subunit RPABC4: I
DNA-directed RNA polymerase II subunit RPB4: J
DNA-directed RNA polymerase II subunit RPB7: K

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
E

E
F

F
H

G
J

H
K

I
L

J
D

K
G

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 polymerases I, II, and III subunit RPABC5

DNA-directed RNA polymerase II subunit RPB11

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

DNA-directed RNA polymerase II subunit RPB4

DNA-directed RNA polymerase II subunit RPB7

Related Entries With Identical Sequence