SMTL ID : 8u9r.1

STRUCTURAL BASIS OF TRANSCRIPTION: RNA POLYMERASE II SUBSTRATE BINDING AND METAL COORDINATION USING A FREE-ELECTRON LASER

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.34 Å

Oligo State

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

Ligands

8 x ZN: ZINC ION

ZN.1: 6 residues within 4Å: Chain A: C.110, C.148, E.149, R.164, G.165, C.167 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:C.167 ZN.2: 5 residues within 4Å: Chain A: C.67, T.69, 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.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.9: 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.10: 4 residues within 4Å: Chain I: C.7, C.10, C.29, C.32 3 PLIP interactions: 3 interactions with chain I Metal complexes: I:C.7, I:C.10, I:C.29 ZN.11: 6 residues within 4Å: Chain I: C.75, C.78, S.80, C.103, C.106, H.108 3 PLIP interactions: 3 interactions with chain I Metal complexes: I:C.75, I:C.106, I:H.108 ZN.12: 4 residues within 4Å: Chain J: C.7, C.10, C.45, C.46 4 PLIP interactions: 4 interactions with chain J Metal complexes: J:C.7, J:C.10, J:C.45, J:C.46 ZN.13: 4 residues within 4Å: Chain L: C.31, C.34, C.48, C.51 4 PLIP interactions: 4 interactions with chain L Metal complexes: L:C.31, L:C.34, L:C.48, L:C.51

1 x GOL: GLYCEROL

GOL.3: 6 residues within 4Å: Chain A: Q.935, K.938, D.939, F.942, R.1023 Chain E: R.207 3 PLIP interactions: 1 interactions with chain E, 2 interactions with chain A Hydrogen bonds: E:R.207, A:D.939, A:R.1023

3 x MG: MAGNESIUM ION

MG.4: 5 residues within 4Å: Chain A: D.481, D.483, D.485 Chain M: G.10 Ligands: ATP.6 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.481, A:D.481, A:D.483, A:D.485 MG.5: 5 residues within 4Å: Chain A: D.481, D.483 Chain B: D.837, R.1020 Ligands: ATP.6 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.481, A:D.483, A:D.483 MG.8: 2 residues within 4Å: Chain B: E.529 Ligands: ATP.6 No protein-ligand interaction detected (PLIP)

1 x ATP: ADENOSINE-5'-TRIPHOSPHATE

ATP.6: 19 residues within 4Å: Chain A: R.446, P.448, N.479, D.481, D.483, D.485, Q.1078, L.1081, H.1085 Chain B: R.766, D.837, K.987, R.1020 Chain M: G.10 Chain N: T.5, C.6 Ligands: MG.4, MG.5, MG.8 12 PLIP interactions: 4 interactions with chain B, 8 interactions with chain A Salt bridges: B:R.766, B:K.987, B:K.987, B:R.1020, A:H.1085, A:H.1085 Hydrogen bonds: A:R.446, A:R.446, A:N.479, A:N.479, A:Q.1078, A:Q.1078

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lin, G. et al., Structural basis of transcription: RNA polymerase II substrate binding and metal coordination using a free-electron laser. Proc.Natl.Acad.Sci.USA (2024)

Release Date

2024-09-18

Peptides

DNA-directed RNA polymerase II subunit RPB1: A
DNA-directed RNA polymerase subunit beta: B
DNA-directed RNA polymerase II subunit RPB3: C
DNA-directed RNA polymerase II subunit RPB4: D
DNA-directed RNA polymerases I, II, and III subunit RPABC1: E
DNA-directed RNA polymerases I, II, and III subunit RPABC2: F
DNA-directed RNA polymerase II subunit RPB7: G
DNA-directed RNA polymerases I, II, and III subunit RPABC3: H
DNA-directed RNA polymerase II subunit RPB9: I
DNA-directed RNA polymerases II subunit RPABC5: J
DNA-directed RNA polymerase II subunit RPB11: K
DNA-directed RNA polymerases II subunit RPABC4: L

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

K
K

L
L

DNA-directed RNA polymerase II subunit RPB1

DNA-directed RNA polymerase subunit beta

DNA-directed RNA polymerase II subunit RPB3

DNA-directed RNA polymerase II subunit RPB4

DNA-directed RNA polymerases I, II, and III subunit RPABC1

DNA-directed RNA polymerases I, II, and III subunit RPABC2

DNA-directed RNA polymerase II subunit RPB7

DNA-directed RNA polymerases I, II, and III subunit RPABC3

DNA-directed RNA polymerase II subunit RPB9

DNA-directed RNA polymerases II subunit RPABC5

DNA-directed RNA polymerase II subunit RPB11

DNA-directed RNA polymerases II subunit RPABC4

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