SMTL ID : 5m3f.1

Yeast RNA polymerase I elongation complex at 3.8A

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

6 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: C.62, T.64, 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.2: 5 residues within 4Å: Chain A: C.102, C.105, C.233, N.235, 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.5: 4 residues within 4Å: Chain B: C.1104, C.1107, C.1128, C.1131 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.1104, B:C.1107, B:C.1128, B:C.1131 ZN.6: 4 residues within 4Å: Chain G: C.10, C.13, C.30, C.33 4 PLIP interactions: 4 interactions with chain G Metal complexes: G:C.10, G:C.13, G:C.30, G:C.33 ZN.7: 4 residues within 4Å: Chain H: C.7, C.10, 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.8: 5 residues within 4Å: Chain J: C.31, C.34, C.48, D.50, C.51 2 PLIP interactions: 2 interactions with chain J Metal complexes: J:C.34, J:C.51

1 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 4 residues within 4Å: Chain A: D.627, D.629, D.631 Chain M: C.20 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.627, A:D.629, A:D.631

1 x SO4: SULFATE ION(Non-functional Binders)

SO4.4: 6 residues within 4Å: Chain B: R.501, H.532, H.544, S.698, I.699, L.700 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:S.698, B:I.699, B:L.700 Salt bridges: B:H.532, B:H.544

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Neyer, S. et al., Structure of RNA polymerase I transcribing ribosomal DNA genes. Nature (2016)

Release Date

2016-11-23

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 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 I subunit RPA12: G
DNA-directed RNA polymerases I, II, and III subunit RPABC5: H
DNA-directed RNA polymerases I and III subunit RPAC2: I
DNA-directed RNA polymerases I, II, and III subunit RPABC4: J
DNA-directed RNA polymerase I subunit RPA49: N
DNA-directed RNA polymerase I subunit RPA34: O
DNA-directed RNA polymerase I subunit RPA14: P
DNA-directed RNA polymerase I subunit RPA43: Q

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

N
M

O
N

P
D

Q
G

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 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 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

DNA-directed RNA polymerase I subunit RPA49

DNA-directed RNA polymerase I subunit RPA34

DNA-directed RNA polymerase I subunit RPA14

DNA-directed RNA polymerase I subunit RPA43

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