8toe.1 | SWISS-MODEL Template Library

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SMTL ID : 8toe.1

Escherichia coli RNA polymerase unwinding intermediate (I1c) at the lambda PR promoter

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-1-1-1-1-mer

Ligands

3 x 1N7: CHAPSO(Non-covalent)

1N7.1:	10 residues within 4Å: Chain C: Q.46, Y.47, Y.179, S.398, A.399, V.400, E.458, E.461, E.583, Y.584 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:Y.179, C:A.399, C:Y.584 Hydrogen bonds: C:S.398, C:V.400
1N7.5:	6 residues within 4Å: Chain C: Q.1264 Chain D: L.255, D.256 Chain F: I.511, F.522 Ligands: 1N7.6 5 PLIP interactions: 2 interactions with chain D, 2 interactions with chain F, 1 interactions with chain C Hydrophobic interactions: D:L.255, F:I.511, F:F.522 Hydrogen bonds: D:D.256, C:Q.1264
1N7.6:	5 residues within 4Å: Chain F: I.505, P.510, I.511, L.519 Ligands: 1N7.5 1 PLIP interactions: 1 interactions with chain F Hydrophobic interactions: F:I.505

1 x MG: MAGNESIUM ION(Non-covalent)

MG.2:

3 residues within 4Å:

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

4 PLIP interactions:

4 interactions with chain D

Metal complexes: D:D.460, D:D.460, D:D.462, D:D.464

2 x ZN: ZINC ION(Non-covalent)

ZN.3:	5 residues within 4Å: Chain D: C.70, C.72, C.85, K.87, 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:	6 residues within 4Å: Chain D: C.814, C.888, D.889, T.890, 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

Saecker, R.M. et al., Early intermediates in bacterial RNA polymerase promoter melting visualized by time-resolved cryo-electron microscopy. Nat.Struct.Mol.Biol. (2024)

Release Date

2024-07-03

Peptides

DNA-directed RNA polymerase subunit alpha: ABG
DNA-directed RNA polymerase subunit beta: C
DNA-directed RNA polymerase subunit beta': D
DNA-directed RNA polymerase subunit omega: E
RNA polymerase sigma factor RpoD: F

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
G

B
H

G
M

C
I

D
J

E
K

F
L

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 factor RpoD

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