SMTL ID : 7eu1.1

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

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

8 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.56, C.59, C.67, H.70 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.56, A:C.59, A:C.67, A:H.70 ZN.3: 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.4: 4 residues within 4Å: Chain B: C.1108, C.1111, C.1133, C.1136 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:C.1111, B:C.1136 ZN.5: 4 residues within 4Å: Chain C: C.90, C.93, C.99, C.102 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:C.90, C:C.99 ZN.6: 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.7: 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.8: 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.9: 4 residues within 4Å: Chain J: C.12, 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.2: 3 residues within 4Å: Chain A: D.447, D.449, D.451 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.447, A:D.449, A:D.451, A:D.451 MG.10: 3 residues within 4Å: Chain K: D.830, D.832, D.834 4 PLIP interactions: 4 interactions with chain K Metal complexes: K:D.830, 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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