SMTL ID : 6o6c.1

RNA polymerase II elongation complex arrested at a CPD lesion

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

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 (5'-R(P*AP*UP*CP*GP*AP*GP*AP*GP*G)-3')(Non-covalent)

A-U-C-G-A-G-A-G-G.1: 24 residues within 4Å: Chain A: R.446, P.448, D.483, G.484, D.485 Chain B: A.477, Q.481, M.773, Q.776, K.979, K.987, R.1096, H.1097 Chain L: T.18, C.19, C.20, T.21, C.22, T.23, C.24, G.25, A.26, T.27 Ligands: MG.4 Protein-ligand interaction information (PLIP) not available

8 x ZN: ZINC ION(Non-covalent)

ZN.2: 5 residues within 4Å: Chain A: C.107, M.108, C.110, C.148, C.167 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:C.107, A:M.108, A:C.167 ZN.3: 5 residues within 4Å: Chain A: C.67, Q.68, C.70, C.77, H.80 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.67, A:C.67, A:C.70, A:H.80 ZN.5: 4 residues within 4Å: Chain B: C.1163, C.1166, C.1182, C.1185 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:C.1163, B:C.1182, B:C.1185 ZN.6: 6 residues within 4Å: Chain C: C.86, C.88, E.89, H.91, C.92, C.95 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:C.86, C:C.92, C:C.95 ZN.7: 3 residues within 4Å: Chain G: N.12, T.31, C.32 3 PLIP interactions: 3 interactions with chain G Metal complexes: G:T.31, G:T.31, G:C.32 ZN.8: 5 residues within 4Å: Chain G: C.75, C.78, C.103, C.106, H.108 2 PLIP interactions: 2 interactions with chain G Metal complexes: G:C.78, G:H.108 ZN.9: 4 residues within 4Å: Chain H: C.7, C.10, C.45, C.46 5 PLIP interactions: 5 interactions with chain H Metal complexes: H:C.7, H:C.10, H:C.45, H:C.45, H:C.46 ZN.10: 5 residues within 4Å: Chain J: C.31, C.34, S.36, D.50, C.51 4 PLIP interactions: 4 interactions with chain J Metal complexes: J:C.31, J:C.34, J:D.50, J:C.51

1 x MG: MAGNESIUM ION(Non-covalent)

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

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lahiri, I. et al., 3.1 angstrom structure of yeast RNA polymerase II elongation complex stalled at a cyclobutane pyrimidine dimer lesion solved using streptavidin affinity grids. J.Struct.Biol. (2019)

Release Date

2019-06-26

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
D

E
E

F
F

G
G

H
H

I
I

J
J

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