SMTL ID : 8him.1

A cryo-EM structure of B. oleracea RNA polymerase V elongation complex at 2.73 Angstrom

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

1 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 3 residues within 4Å: Chain D: D.449, D.451, D.453 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:D.449, D:D.451, D:D.453

6 x ZN: ZINC ION(Non-covalent)

ZN.2: 4 residues within 4Å: Chain D: H.938, H.940, C.989, C.1004 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:H.938, D:H.940, D:C.989, D:C.1004 ZN.3: 5 residues within 4Å: Chain E: C.91, A.93, C.94, C.100, C.103 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:C.91, E:C.94, E:C.100, E:C.103 ZN.4: 4 residues within 4Å: Chain G: C.7, C.10, C.44, C.45 4 PLIP interactions: 4 interactions with chain G Metal complexes: G:C.7, G:C.10, G:C.44, G:C.45 ZN.5: 4 residues within 4Å: Chain I: C.12, C.15, C.29, C.32 4 PLIP interactions: 4 interactions with chain I Metal complexes: I:C.12, I:C.15, I:C.29, I:C.32 ZN.6: 4 residues within 4Å: Chain K: R.75, Q.80, H.81, G.82 No protein-ligand interaction detected (PLIP) ZN.7: 4 residues within 4Å: Chain K: C.7, C.10, C.29, C.32 3 PLIP interactions: 3 interactions with chain K Metal complexes: K:C.7, K:C.29, K:C.32

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Xie, G. et al., Structure and mechanism of the plant RNA polymerase V. Science (2023)

Release Date

2023-03-22

Peptides

DNA-directed RNA polymerase V largest subunit: D
RPOLD domain-containing protein: E
DNA-directed RNA polymerases I, II, and III subunit RPABC2: F
DNA-directed RNA polymerases I, II, and III subunit RPABC5: G
RNA_pol_L_2 domain-containing protein: H
DNA-directed RNA polymerases II, IV and V subunit 12: I
DNA-directed RNA polymerases I, II, and III subunit RPABC3: J
DNA-directed RNA polymerase subunit: K
DNA-directed RNA polymerases I, II, and III subunit RPABC1: L
DNA-directed RNA polymerase IV and V subunit 2: M

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

D
A

E
C

F
F

G
J

H
K

I
L

J
H

K
I

L
E

M
B

DNA-directed RNA polymerase V largest subunit

RPOLD domain-containing protein

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

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

RNA_pol_L_2 domain-containing protein

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

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

DNA-directed RNA polymerase subunit

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

DNA-directed RNA polymerase IV and V subunit 2

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