SMTL ID : 9msf.1

de novo SigN RNA polymerase transcription initiation intermediate with post-catalytic bEBP state (RPi1 closed ring)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-6-2-1-1-1-1-mer

Ligands

5 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.1: 20 residues within 4Å: Chain A: Y.20, V.21, E.49, S.50, G.51, V.52, G.53, K.54, E.55, V.56, N.161, L.201, H.204, F.205, V.237, R.238, K.241 Chain B: D.176, R.180 Ligands: MG.2 20 PLIP interactions: 19 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:V.21, A:V.21, A:G.51, A:V.52, A:G.53, A:K.54, A:E.55, A:V.56, A:N.161, A:K.241, A:K.241 Water bridges: A:R.194, A:R.194 Salt bridges: A:K.54, A:K.54, A:R.238, A:R.238, A:R.238, B:R.180 pi-Stacking: A:Y.20 ATP.3: 17 residues within 4Å: Chain B: Y.20, V.21, F.22, S.50, G.51, V.52, G.53, K.54, E.55, D.119, E.120, L.201, F.205, V.237, R.238, K.241 Chain C: R.180 19 PLIP interactions: 17 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:V.21, B:V.21, B:G.51, B:V.52, B:G.53, B:K.54, B:E.55, B:E.55, B:V.56, B:D.119, B:E.120 Water bridges: B:K.54, C:R.180 Salt bridges: B:K.54, B:K.54, B:R.238, B:R.238, C:R.180 pi-Stacking: B:Y.20 ATP.4: 14 residues within 4Å: Chain C: Y.20, V.21, G.51, V.52, G.53, K.54, E.55, V.56, D.119, L.201, V.237, R.238 Chain D: E.137, R.180 18 PLIP interactions: 16 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:V.21, C:V.21, C:E.49, C:G.51, C:V.52, C:G.53, C:K.54, C:E.55, C:E.55, C:V.56, C:D.119 Salt bridges: C:K.54, C:K.54, C:R.238, C:R.238, D:R.180 pi-Stacking: C:Y.20 Water bridges: D:R.180 ATP.5: 14 residues within 4Å: Chain D: Y.20, V.21, G.51, V.52, G.53, K.54, E.55, V.56, D.119, L.201, F.205, V.237, R.238 Chain E: R.180 14 PLIP interactions: 13 interactions with chain D, 1 interactions with chain E Hydrogen bonds: D:V.21, D:V.21, D:G.51, D:V.52, D:G.53, D:K.54, D:E.55, D:V.56, E:R.180 Salt bridges: D:K.54, D:K.54, D:R.238, D:R.238 pi-Stacking: D:Y.20 ATP.7: 17 residues within 4Å: Chain F: Y.20, V.21, F.22, E.49, S.50, G.51, V.52, G.53, K.54, E.55, V.56, D.119, L.201, F.205, V.237, R.238, K.241 19 PLIP interactions: 19 interactions with chain F Hydrogen bonds: F:V.21, F:V.21, F:E.49, F:G.51, F:V.52, F:G.53, F:K.54, F:E.55, F:E.55, F:E.55, F:V.56, F:D.119, F:D.119, F:K.241 Salt bridges: F:K.54, F:K.54, F:R.238, F:R.238 pi-Stacking: F:Y.20

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: D.119 Chain B: R.180 Ligands: ATP.1 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.119 MG.9: 3 residues within 4Å: Chain J: D.460, D.462, D.464 6 PLIP interactions: 3 interactions with chain J, 3 Ligand-Water interactions Metal complexes: J:D.460, J:D.462, J:D.464, H2O.24, H2O.29, H2O.30

1 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.6: 14 residues within 4Å: Chain E: Y.20, V.21, F.22, S.50, G.51, V.52, G.53, K.54, E.55, V.56, L.201, V.237, R.238, K.241 12 PLIP interactions: 12 interactions with chain E Hydrogen bonds: E:V.21, E:V.21, E:G.51, E:V.52, E:G.53, E:K.54, E:E.55, E:E.55, E:V.56, E:K.241 Salt bridges: E:K.54, E:R.238

1 x POP: PYROPHOSPHATE 2-(Non-covalent)

POP.8: 4 residues within 4Å: Chain I: R.678, S.1105, R.1106 Chain J: R.731 5 PLIP interactions: 4 interactions with chain I, 1 interactions with chain J Hydrogen bonds: I:R.678, I:S.1105 Water bridges: I:R.1106 Salt bridges: I:R.1106, J:R.731

2 x ZN: ZINC ION(Non-covalent)

ZN.10: 5 residues within 4Å: Chain J: C.70, C.72, G.73, C.85, C.88 4 PLIP interactions: 4 interactions with chain J Metal complexes: J:C.70, J:C.72, J:C.85, J:C.88 ZN.11: 4 residues within 4Å: Chain J: C.814, C.888, C.895, C.898 4 PLIP interactions: 4 interactions with chain J Metal complexes: J:C.814, J:C.888, J:C.895, J:C.898

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mueller, A.U. et al., Real-time capture of sigma N transcription initiation intermediates reveals mechanism of ATPase-driven activation by limited unfolding. Nat Commun (2025)

Release Date

2025-08-13

Peptides

Transcriptional regulator (NtrC family): ABCDEF
DNA-directed RNA polymerase subunit alpha: GH
DNA-directed RNA polymerase subunit beta: I
DNA-directed RNA polymerase subunit beta': J
DNA-directed RNA polymerase subunit omega: K
RNA polymerase sigma-54 factor: L

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
M

Transcriptional regulator (NtrC family)

DNA-directed RNA polymerase subunit alpha

DNA-directed RNA polymerase subunit beta

DNA-directed RNA polymerase subunit beta'

DNA-directed RNA polymerase subunit omega

RNA polymerase sigma-54 factor

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