SMTL ID : 7eu0.1

The cryo-EM structure of A. thaliana Pol IV-RDR2 backtracked complex

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

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

C-C-G-A.1: 24 residues within 4Å: Chain K: R.417, S.475, S.477, Q.478, G.519, S.523, A.524, Q.582, R.584, K.589, K.783, P.785, D.830, D.832, G.833, D.834, G.1045, D.1046, D.1049 Chain M: U.35, C.36, G.37, G.38 Ligands: MG.11 Protein-ligand interaction information (PLIP) not available

8 x ZN: ZINC ION(Non-covalent)

ZN.2: 4 residues within 4Å: Chain A: C.56, C.59, C.67, H.70 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:C.56, A:C.67, A:H.70 ZN.4: 4 residues within 4Å: Chain A: H.983, H.985, C.1031, C.1044 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.983, A:H.985, A:C.1031, A:C.1044 ZN.5: 4 residues within 4Å: Chain B: C.1108, C.1111, C.1133, C.1136 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.1108, B:C.1111, B:C.1133, B:C.1136 ZN.6: 4 residues within 4Å: Chain C: C.90, C.93, C.99, C.102 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:C.90, C:C.93, C:C.102 ZN.7: 4 residues within 4Å: Chain G: C.76, C.79, C.103, C.108 4 PLIP interactions: 4 interactions with chain G Metal complexes: G:C.76, G:C.79, G:C.103, G:C.108 ZN.8: 4 residues within 4Å: Chain G: C.7, C.10, C.29, C.32 4 PLIP interactions: 4 interactions with chain G Metal complexes: G:C.7, G:C.10, G:C.29, G:C.32 ZN.9: 5 residues within 4Å: Chain H: C.7, C.10, G.11, 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.10: 5 residues within 4Å: Chain J: C.12, G.13, C.15, C.29, C.32 4 PLIP interactions: 4 interactions with chain J Metal complexes: J:C.12, J:C.15, J:C.29, J:C.32

2 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 4 residues within 4Å: Chain A: D.447, D.449, D.451 Chain M: C.16 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.447, A:D.447, A:D.449, A:D.451 MG.11: 4 residues within 4Å: Chain K: D.830, D.832, D.834 Ligands: C-C-G-A.1 3 PLIP interactions: 3 interactions with chain K Metal complexes: K:D.830, K:D.832, K:D.834

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Huang, K. et al., Pol IV and RDR2: A two-RNA-polymerase machine that produces double-stranded RNA. Science (2021)

Release Date

2021-12-29

Peptides

DNA-directed RNA polymerase IV subunit 1: A
DNA-directed RNA polymerases IV and V subunit 2: B
DNA-directed RNA polymerases II, IV and V subunit 3: C
DNA-directed RNA polymerases II and IV subunit 5A: D
DNA-directed RNA polymerases II, IV and V subunit 6A: E
DNA-directed RNA polymerases II, IV and V subunit 8B: F
DNA-directed RNA polymerases II, IV and V subunit 9A: G
DNA-directed RNA polymerases II, IV and V subunit 10: H
DNA-directed RNA polymerases II, IV and V subunit 11: I
DNA-directed RNA polymerases II, IV and V subunit 12: J
RNA-dependent RNA polymerase 2: K

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
M

DNA-directed RNA polymerase IV subunit 1

DNA-directed RNA polymerases IV and V subunit 2

DNA-directed RNA polymerases II, IV and V subunit 3

DNA-directed RNA polymerases II and IV subunit 5A

DNA-directed RNA polymerases II, IV and V subunit 6A

DNA-directed RNA polymerases II, IV and V subunit 8B

DNA-directed RNA polymerases II, IV and V subunit 9A

DNA-directed RNA polymerases II, IV and V subunit 10

DNA-directed RNA polymerases II, IV and V subunit 11

DNA-directed RNA polymerases II, IV and V subunit 12

RNA-dependent RNA polymerase 2

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