SMTL ID : 5w51.1

Pol II elongation complex with an N6-methyladenine-containing template and a matched UMPNPP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.40 Å

Oligo State

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

Ligands

1 x A- U- G- G- A- G- A- G- G: 9mer RNA(Non-covalent)

A-U-G-G-A-G-A-G-G.1: 28 residues within 4Å: Chain A: R.320, R.350, R.446, Q.447, P.448, D.481, D.483, D.485 Chain B: G.478, Q.481, E.529, Q.776, K.979, K.987, H.1097 Chain K: A.19, C.20, C.21, T.22, C.23, T.24, C.25, C.26, A.27, T.28, G.29 Ligands: MG.4, 2KH.6 Protein-ligand interaction information (PLIP) not available

8 x ZN: ZINC ION(Non-covalent)

ZN.2: 5 residues within 4Å: Chain A: C.107, H.109, C.110, C.148, C.167 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.109, A:C.110, A:C.148 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.70, A:C.77, A:H.80 ZN.7: 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.8: 4 residues within 4Å: Chain C: C.86, C.88, 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: 5 residues within 4Å: Chain G: C.7, C.10, C.29, T.31, 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: 5 residues within 4Å: Chain H: C.7, C.10, R.43, 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: 5 residues within 4Å: Chain A: D.481, D.483, D.485 Ligands: A-U-G-G-A-G-A-G-G.1, 2KH.6 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.481, A:D.483, A:D.485 MG.5: 4 residues within 4Å: Chain A: D.481 Chain B: E.836, R.1020 Ligands: 2KH.6 No protein-ligand interaction detected (PLIP)

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

2KH.6: 12 residues within 4Å: Chain A: R.446, P.448, N.479, D.481, D.483 Chain B: R.766, K.987, R.1020 Chain K: A.19 Ligands: A-U-G-G-A-G-A-G-G.1, MG.4, MG.5 9 PLIP interactions: 5 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:K.987, B:R.1020, A:R.446, A:N.479, A:D.483, A:D.483 Salt bridges: B:R.766, B:K.987, B:R.1020

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, W. et al., Epigenetic DNA Modification N6-Methyladenine Causes Site-Specific RNA Polymerase II Transcriptional Pausing. J.Am.Chem.Soc. (2017)

Release Date

2018-06-20

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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