SMTL ID : 7vba.1

Structure of the pre state human RNA Polymerase I Elongation Complex

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

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

U-G-C-U-G-A-C-U.1: 29 residues within 4Å: Chain A: K.430, R.552, D.590, G.591, D.592 Chain B: R.180, S.451, G.452, V.455, R.464, H.473, M.511, Q.690, Q.694, K.882, K.890, H.1004, K.1009 Chain N: A.14, G.15, T.16, C.17, A.18, G.19, C.20, A.21, A.22 Ligands: MG.4, 2TM.5 Protein-ligand interaction information (PLIP) not available

5 x ZN: ZINC ION(Non-covalent)

ZN.2: 5 residues within 4Å: Chain A: C.64, T.66, C.67, C.74, H.77 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:C.64, A:C.67, A:C.74 ZN.3: 4 residues within 4Å: Chain A: C.104, C.107, C.205, C.208 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:C.104, A:C.107, A:C.205 ZN.6: 4 residues within 4Å: Chain B: C.1070, C.1073, C.1098, C.1101 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.1070, B:C.1073, B:C.1098, B:C.1101 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: 6 residues within 4Å: Chain J: C.19, C.22, T.24, C.36, R.37, C.39 3 PLIP interactions: 3 interactions with chain J Metal complexes: J:C.19, J:C.36, J:C.39

1 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 5 residues within 4Å: Chain A: D.588, D.590, D.592 Ligands: U-G-C-U-G-A-C-U.1, 2TM.5 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.590, A:D.590

1 x 2TM: 5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}phosphoryl]cytidine(Non-covalent)

2TM.5: 10 residues within 4Å: Chain A: R.552, P.554, N.586, D.588, Q.1225 Chain B: R.684 Chain N: G.13, A.14 Ligands: U-G-C-U-G-A-C-U.1, MG.4 6 PLIP interactions: 2 interactions with chain B, 4 interactions with chain A Salt bridges: B:R.684, B:R.923 Hydrogen bonds: A:R.552, A:R.552, A:N.586, A:D.588

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhao, D. et al., Structure of the human RNA polymerase I elongation complex. Cell Discov (2021)

Release Date

2022-02-16

Peptides

DNA-directed RNA polymerase I subunit RPA1: A
DNA-directed RNA polymerase I subunit RPA2: 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 RPA34: K
DNA-directed RNA polymerase I subunit RPA43: L
DNA-directed RNA polymerase I subunit RPA49: M

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

K
N

L
G

M
M

DNA-directed RNA polymerase I subunit RPA1

DNA-directed RNA polymerase I subunit RPA2

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 RPA34

DNA-directed RNA polymerase I subunit RPA43

DNA-directed RNA polymerase I subunit RPA49

Related Entries With Identical Sequence