SMTL ID : 9epc.1

Cryo-EM structure of the Plastid-encoded RNA polymerase from Sinapis alba

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 3.00 Å

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 DTT: 2,3-DIHYDROXY-1,4-DITHIOBUTANE(Non-covalent)

DTT.1: 6 residues within 4Å: Chain D: R.548, C.551 Chain E: M.121, P.124 Chain J: A.286 Chain M: D.317 No protein-ligand interaction detected (PLIP)

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.75, H.128, W.177, D.212, H.216 4 PLIP interactions: 4 interactions with chain I Metal complexes: I:H.75, I:H.128, I:D.212, I:H.216 FE.7: 6 residues within 4Å: Chain N: H.72, H.124, W.173, D.223, W.225, H.227 4 PLIP interactions: 4 interactions with chain N Metal complexes: N:H.124, N:D.223, N:D.223, N:H.227

2 x CA: CALCIUM ION(Non-covalent)

CA.4: 3 residues within 4Å: Chain K: D.267, N.269, E.296 2 PLIP interactions: 2 interactions with chain K Metal complexes: K:D.267, K:E.296 CA.8: 4 residues within 4Å: Chain S: P.246, D.376, N.378, E.405 2 PLIP interactions: 2 interactions with chain S Metal complexes: S:D.376, S:E.405

1 x K: POTASSIUM ION(Non-covalent)

K.5: 5 residues within 4Å: Chain K: D.388, T.390, S.431, T.434, G.436 4 PLIP interactions: 4 interactions with chain K Metal complexes: K:T.390, K:S.431, K:T.434, K:G.436

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

SAH.6: 12 residues within 4Å: Chain L: G.101, F.102, S.195, T.259, R.260, D.283, M.284, N.286, H.287, Y.324, Y.337, F.339 11 PLIP interactions: 10 interactions with chain L, 1 interactions with chain R Hydrogen bonds: L:F.102, L:F.102, L:S.195, L:S.195, L:H.287, L:H.287, L:Y.324 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

Effantin, G. et al., Cryo-EM structure of the Plastid-encoded RNA polymerase from Sinapis alba. To Be Published

Release Date

2025-06-18

Peptides

DNA-directed RNA polymerase subunit alpha: AB
RpoB, subunit beta: C
DNA-directed RNA polymerase subunit beta': D
DNA-directed RNA polymerase subunit beta'': E
PAP1, pTAC3: F
PAP2, pTAC2: G
PAP3, pTAC10: H
PAP4, FSD3: I
PAP5, pTAC12, HEMERA: J
PAP6, FLN1: K
PAP7, pTAC14: L
PAP8, pTAC6: M
PAP9, FSD2: N
PAP10, TRXz: OP
PAP11, MurE-like: Q
PAP12, pTAC7: R
FLN2: S
pTAC18: T
PRIN2, PLASTID REDOX INSENSITIVE 2: 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

RpoB, subunit beta

DNA-directed RNA polymerase subunit beta'

DNA-directed RNA polymerase subunit beta''

PAP1, pTAC3

PAP2, pTAC2

PAP3, pTAC10

PAP4, FSD3

PAP5, pTAC12, HEMERA

PAP6, FLN1

PAP7, pTAC14

PAP8, pTAC6

PAP9, FSD2

PAP10, TRXz

PAP11, MurE-like

PAP12, pTAC7

FLN2

pTAC18

PRIN2, PLASTID REDOX INSENSITIVE 2

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