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SMTL ID : 8to1.1

Escherichia coli RNA polymerase unwinding intermediate (I1a) at the lambda PR promoter

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

4 x 4QM: (3R,5S,7R,8R,9S,10S,12S,13R,14S,17R)-10,13-dimethyl-17-[(2R)-pentan-2-yl]-2,3,4,5,6,7,8,9,11,12,14,15,16,17-tetradecahydro-1H-cyclopenta[a]phenanthrene-3,7,12-triol(Non-covalent)

4QM.1:	6 residues within 4Å: Chain A: E.72, D.135 Chain C: Q.725, Y.726, E.962, I.966 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain A Hydrophobic interactions: C:Y.726, C:Y.726, C:E.962 Hydrogen bonds: A:D.135
4QM.2:	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 10 PLIP interactions: 10 interactions with chain C Hydrophobic interactions: C:Y.47, C:Y.179, C:A.399, C:E.458, C:E.583, C:Y.584 Hydrogen bonds: C:Q.46, C:S.398, C:A.399, C:V.400
4QM.6:	4 residues within 4Å: Chain D: D.256 Chain F: I.511, F.522 Ligands: 4QM.7 3 PLIP interactions: 3 interactions with chain F Hydrophobic interactions: F:I.511, F:I.511, F:F.522
4QM.7:	6 residues within 4Å: Chain D: R.259 Chain F: I.505, P.510, I.511, L.519 Ligands: 4QM.6 3 PLIP interactions: 3 interactions with chain F Hydrophobic interactions: F:I.505, F:I.511, F:L.519

1 x MG: MAGNESIUM ION(Non-covalent)

MG.3:

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.4:	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.5:	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

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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3iyd.1 | 3lu0.1 | 4jk1.1 | 4jk1.2 | 4jk2.1 | 4jk2.2 | 4jkr.1 | 4jkr.2 | 4kmu.1 | 4kmu.2 | 4kn4.1 | 4kn4.2 | 4kn7.1 | 4kn7.2 | 4ljz.1 | 4ljz.2 | 4lk0.1 | 4lk0.2 | 4lk1.1 | 4lk1.2 | 4llg.1 | 4llg.2 | 4mex.1 | 4mex.2 | 4mey.1 | 4mey.2 | 4s20.1 | 4s20.2 | 4xsx.1 | 4xsx.2 more...less...

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