SMTL ID : 8qeq.1

RNA polymerase II bound to minimal Alu RNA right arm in the alternative conformation

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

7 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: C.71, T.73, C.74, C.81, H.84 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.71, A:C.74, A:C.81, A:H.84 ZN.2: 5 residues within 4Å: Chain A: C.111, C.114, C.154, G.183, C.184 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:C.111, A:C.114, A:C.154, A:G.183, A:C.184 ZN.4: 4 residues within 4Å: Chain B: C.1119, C.1122, C.1137, C.1140 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.1119, B:C.1122, B:C.1137, B:C.1140 ZN.5: 4 residues within 4Å: Chain G: C.17, C.20, C.39, C.42 4 PLIP interactions: 4 interactions with chain G Metal complexes: G:C.17, G:C.20, G:C.39, G:C.42 ZN.6: 4 residues within 4Å: Chain G: C.86, C.89, C.114, C.119 4 PLIP interactions: 4 interactions with chain G Metal complexes: G:C.86, G:C.89, G:C.114, G:C.119 ZN.7: 4 residues within 4Å: Chain H: C.7, C.10, C.44, C.45 4 PLIP interactions: 4 interactions with chain H Metal complexes: H:C.7, H:C.10, H:C.44, H:C.45 ZN.8: 4 residues within 4Å: Chain J: C.19, C.22, C.36, C.39 4 PLIP interactions: 4 interactions with chain J Metal complexes: J:C.19, J:C.22, J:C.36, J:C.39

1 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 4 residues within 4Å: Chain A: D.495, D.497, D.499 Chain K: C.76 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.495, A:D.497, A:D.499, A:D.499

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tluckova, K. et al., Mechanism of mammalian transcriptional repression by noncoding RNA. To Be Published

Release Date

2024-12-11

Peptides

DNA-directed RNA polymerase subunit: A
DNA-directed RNA polymerase subunit beta: B
DNA-directed RNA polymerase II subunit RPB3: C
DNA-directed RNA polymerase II subunit E: D
DNA-directed RNA polymerase II subunit F: 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
RNA_pol_L_2 domain-containing protein: I
RNA polymerase II subunit K: 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 subunit

DNA-directed RNA polymerase subunit beta

DNA-directed RNA polymerase II subunit RPB3

DNA-directed RNA polymerase II subunit E

DNA-directed RNA polymerase II subunit F

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

RNA_pol_L_2 domain-containing protein

RNA polymerase II subunit K

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