SMTL ID : 6bm4.1

Pol II elongation complex with an abasic lesion at i-1 position,soaking UMPNPP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.95 Å

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- A: RNA (5'-R(*AP*UP*CP*AP*AP*GP*AP*GP*A)-3')(Non-covalent)

A-U-C-G-A-G-A-G-A.1: 26 residues within 4Å: Chain A: R.320, K.323, R.350, R.446, D.481, D.483, D.485 Chain B: N.465, R.476, A.477, G.478, Q.481, Q.776, K.979, K.987, H.1097 Chain K: C.21, T.22, C.23, T.24, C.25, G.26, A.27, T.28, G.29 Ligands: MG.4 Protein-ligand interaction information (PLIP) not available

8 x ZN: ZINC ION(Non-covalent)

ZN.2: 6 residues within 4Å: Chain A: C.107, M.108, C.110, C.148, C.167, N.169 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 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:C.67, A:C.77, A:H.80 ZN.6: 4 residues within 4Å: Chain B: C.1163, C.1166, C.1182, C.1185 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:C.1163, B:C.1166 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 G: C.7, 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.10: 4 residues within 4Å: Chain G: C.75, C.78, C.103, C.106 4 PLIP interactions: 4 interactions with chain G Metal complexes: G:C.75, G:C.78, G:C.103, G:C.106 ZN.11: 4 residues within 4Å: Chain H: C.7, C.10, C.45, C.46 4 PLIP interactions: 4 interactions with chain H Metal complexes: H:C.7, H:C.10, H:C.45, H:C.46 ZN.12: 4 residues within 4Å: Chain J: C.31, C.34, C.48, C.51 4 PLIP interactions: 4 interactions with chain J Metal complexes: J:C.31, J:C.34, J:C.48, J:C.51

2 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-A.1 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.481, A:D.483, A:D.485 MG.5: 2 residues within 4Å: Chain A: D.481 Ligands: 2KH.7 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.481

1 x 2KH: 5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]uridine(Non-covalent)

2KH.7: 8 residues within 4Å: Chain A: D.481, D.483, K.752 Chain B: R.766, K.987, S.1019, R.1020 Ligands: MG.5 8 PLIP interactions: 2 interactions with chain A, 6 interactions with chain B Hydrogen bonds: A:D.483, A:K.752, B:S.1019, B:S.1019, B:R.1020, B:R.1020 Salt bridges: B:R.766, B:R.1020

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, W. et al., Structural basis of transcriptional stalling and bypass of abasic DNA lesion by RNA polymerase II. Proc. Natl. Acad. Sci. U.S.A. (2018)

Release Date

2018-02-28

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

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