SMTL ID : 8rdj.1

Plastid-encoded RNA polymerase transcription elongation complex (Integrated model)

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-1-1-1-1-1-1-1-1-1-1-1-1-2-1-1-1-1-1-mer

Ligands

1 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain D: D.489, D.491, D.493 Chain X: G.40 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:D.489, D:D.491, D:D.493, D:D.493

1 x ZN: ZINC ION(Non-covalent)

ZN.2: 5 residues within 4Å: Chain E: C.220, R.288, C.293, C.300, C.303 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:C.220, E:C.293, E:C.300, E:C.303

2 x FE: FE (III) ION(Non-covalent)

FE.3: 5 residues within 4Å: Chain I: H.74, H.127, W.176, D.211, H.215 4 PLIP interactions: 3 interactions with chain I, 1 Ligand-Water interactions Metal complexes: I:H.74, I:H.127, I:D.211, H2O.6 FE.5: 5 residues within 4Å: Chain N: H.72, H.124, W.173, D.223, H.227 5 PLIP interactions: 4 interactions with chain N, 1 Ligand-Water interactions Metal complexes: N:H.72, N:H.124, N:D.223, N:H.227, H2O.9

1 x SAH: S-ADENOSYL-L-HOMOCYSTEINE(Non-covalent)

SAH.4: 15 residues within 4Å: Chain L: G.101, F.102, P.189, S.195, T.259, R.260, D.283, M.284, N.286, H.287, Y.324, Y.337, G.338, F.339 Chain R: R.49 13 PLIP interactions: 12 interactions with chain L, 1 interactions with chain R Hydrogen bonds: L:F.102, L:F.102, L:F.102, L:S.195, L:H.287, L:H.287, L:Y.337 Water bridges: L:T.259, L:T.259 Salt bridges: L:R.260, R:R.49 pi-Stacking: L:F.339, L:F.339

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Vergara-Cruces, A. et al., Structure of the plant plastid-encoded RNA polymerase. Cell (2024)

Release Date

2024-03-13

Peptides

DNA-directed RNA polymerase subunit alpha: AB
DNA-directed RNA polymerase subunit beta: C
DNA-directed RNA polymerase subunit beta': D
DNA-directed RNA polymerase subunit beta'': E
PAP1: F
PAP2: G
PAP3: H
PAP4: I
PAP5: J
PAP6: K
PAP7: L
PAP8: M
PAP9: N
PAP10: OP
PAP11: Q
PAP12: R
FLN2: S
PTAC18: T
PRIN2: U

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

I
I

J
J

K
K

L
L

M
M

N
N

O
O

P
P

Q
Q

R
R

S
S

T
T

U
U

DNA-directed RNA polymerase subunit alpha

DNA-directed RNA polymerase subunit beta

DNA-directed RNA polymerase subunit beta'

DNA-directed RNA polymerase subunit beta''

PAP1

PAP2

PAP3

PAP4

PAP5

PAP6

PAP7

PAP8

PAP9

PAP10

PAP11

PAP12

FLN2

PTAC18

PRIN2

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