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SMTL ID : 9msh.1

de novo SigN RNA polymerase open complex (RPo)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

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

POP.1:

3 residues within 4Å:

Chain C: S.1105, R.1106
Chain D: R.731

3 PLIP interactions:

2 interactions with chain C, 1 interactions with chain D

Hydrogen bonds: C:S.1105
Salt bridges: C:R.1106, D:R.731

1 x MG: MAGNESIUM ION(Non-covalent)

MG.2:

3 residues within 4Å:

Chain D: D.460, D.462, D.464

6 PLIP interactions:

3 interactions with chain D, 3 Ligand-Water interactions

Metal complexes: D:D.460, D:D.462, D:D.464, H₂O.9, H₂O.9, H₂O.11

2 x ZN: ZINC ION(Non-covalent)

ZN.3:	4 residues within 4Å: Chain D: C.70, C.72, C.85, C.88 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.70, D:C.72, D:C.85, D:C.88
ZN.4:	5 residues within 4Å: Chain D: C.814, R.883, C.888, C.895, C.898 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.814, D:C.888, D:C.895, D: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

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 omega: E
RNA polymerase sigma-54 factor: F

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
G

B
H

C
I

D
J

E
K

F
M

Export Alignment

Secondary Structure
NoneDSSPPSIPREDSSpro

Colour Scheme

Fade MismatchesEnhance Mismatches

ChainUnique ChainRainbow2° StructureBfactorBfactor RangeSOAEntropyClustalHydrophobicSizeChargedPolarProlineSer/ThrCysteineAliphaticAromaticNo Colour

Background

3D Viewer
NGLPV2D

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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