SMTL ID : 9bw0.1

RNA Polymerase II - No ATP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.51 Å

Oligo State

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

Ligands

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

U-C-G-A-G-A-A-G-G.1: 21 residues within 4Å: Chain A: R.446, Q.447, D.481, D.483, G.484, D.485 Chain B: A.477, G.478, Q.481, Q.776, K.979, H.1097 Chain M: C.5, C.6, C.7, T.8, C.9, T.10, C.11, G.12, A.13 Protein-ligand interaction information (PLIP) not available

8 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.148 ZN.3: 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.4: 5 residues within 4Å: Chain B: C.1163, I.1165, C.1166, C.1182, C.1185 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:C.1163, B:C.1166, B:C.1185 ZN.5: 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.6: 4 residues within 4Å: Chain I: C.7, C.10, C.29, C.32 4 PLIP interactions: 4 interactions with chain I Metal complexes: I:C.7, I:C.10, I:C.29, I:C.32 ZN.7: 5 residues within 4Å: Chain I: C.75, C.78, S.80, C.103, C.106 3 PLIP interactions: 3 interactions with chain I Metal complexes: I:C.75, I:C.78, I:C.103 ZN.8: 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.9: 4 residues within 4Å: Chain L: C.31, E.33, C.34, C.51 3 PLIP interactions: 3 interactions with chain L Metal complexes: L:C.31, L:C.34, L:C.51

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

2024-10-02

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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