SMTL ID : 6hlr.1

Yeast RNA polymerase I elongation complex bound to nucleotide analog GMPCPP (core focused)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

1 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: D.627, D.629, D.631 Chain M: C.20 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.627, A:D.627, A:D.629, A:D.631, A:D.631

6 x ZN: ZINC ION(Non-covalent)

ZN.2: 4 residues within 4Å: Chain A: C.62, C.65, C.72, H.75 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.62, A:C.65, A:C.72, A:H.75 ZN.3: 4 residues within 4Å: Chain A: C.102, C.105, C.233, C.236 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.102, A:C.105, A:C.233, A:C.236 ZN.4: 5 residues within 4Å: Chain B: C.1104, E.1106, C.1107, C.1128, C.1131 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:C.1104, B:C.1107, B:C.1128 ZN.5: 4 residues within 4Å: Chain I: C.10, C.13, C.30, C.33 3 PLIP interactions: 3 interactions with chain I Metal complexes: I:C.10, I:C.13, I:C.30 ZN.6: 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.7: 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 G2P: PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER(Non-covalent)

G2P.8: 10 residues within 4Å: Chain A: R.591, P.593, L.1202 Chain B: R.714, Y.717, S.956, R.957 Chain M: C.20 Chain O: C.15, G.16 8 PLIP interactions: 3 interactions with chain A, 5 interactions with chain B Hydrogen bonds: A:R.591, A:R.591, B:R.714, B:R.714, B:S.956, B:S.956 Salt bridges: A:K.934, B:R.957

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tafur, L. et al., The cryo-EM structure of a 12-subunit variant of RNA polymerase I reveals dissociation of the A49-A34.5 heterodimer and rearrangement of subunit A12.2. Elife (2019)

Release Date

2019-04-03

Peptides

DNA-directed RNA polymerase I subunit RPA190: A
DNA-directed RNA polymerase I subunit RPA135: B
DNA-directed RNA polymerases I and III subunit RPAC1: C
DNA-directed RNA polymerase I subunit RPA14: 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 I subunit RPA43: G
DNA-directed RNA polymerases I, II, and III subunit RPABC3: H
DNA-directed RNA polymerase I subunit RPA12: I
DNA-directed RNA polymerases I, II, and III subunit RPABC5: J
DNA-directed RNA polymerases I and III subunit RPAC2: K
DNA-directed RNA polymerases I, II, and III 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 I subunit RPA190

DNA-directed RNA polymerase I subunit RPA135

DNA-directed RNA polymerases I and III subunit RPAC1

DNA-directed RNA polymerase I subunit RPA14

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

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

DNA-directed RNA polymerase I subunit RPA43

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

DNA-directed RNA polymerase I subunit RPA12

DNA-directed RNA polymerases I, II, and III subunit RPABC5

DNA-directed RNA polymerases I and III subunit RPAC2

DNA-directed RNA polymerases I, II, and III subunit RPABC4

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